Taxonomic assessment of Lumbricidae (Oligochaeta) earthworm genera using DNA barcodes

Pérez-Losada, 2009, Phylogenetic assessment of the earthworm Aporrectodea caliginosa species complex (Oligochaeta, Lumbricidae) based on mitochondrial and nuclear DNA sequences, Mol. Phylogenet. Evol., 52, 293, 10.1016/j.ympev.2009.04.003 Briones, 2009, Are the sexual, somatic and genetic characters enough to solve nomenclatural problems in lumbricid taxonomy?, Soil Biol. Biochem., 41, 2257, 10.1016/j.soilbio.2009.07.008 Edwards, 2004 Edwards, 1996 Lavelle, 2001 M.B. Bouché, Strategies lombriciennes, in: U. Lohm, T. Persson (Eds.), Soil Organisms as Components of Ecosystems, Stockholm, 1977, p. 122–132. Lee, 1985 Thakuria, 2010, Gut wall bacteria of earthworms: a natural selection process, ISME J, 4, 357, 10.1038/ismej.2009.124 Pop, 2003, Use of 18S, 16S rDNA and cytochrome c oxidase sequences in earthworm taxonomy (Oligochaeta, Lumbricidae), Pedobiologia, 47, 428 Jamieson, 2006, Non-leech Clitellata (with contributions by Marco Ferraguti), 235 Jamieson, 1988, On the phylogeny and higher classification of the Oligochaeta, Cladistics, 4, 367, 10.1111/j.1096-0031.1988.tb00520.x Gates, 1975, Contributions to a revision of the earthworm family Lumbricidae. XII. Enterion mammale Savigny, 1826 and its position in the family, Megadrilogica, 2, 1 Bouché, 1972, Lombriciens de France. Écologie et Systématique (n hors-série), Institut National de la Recherche Agronomique, Annales de Zoologie-Écologie Animale Omodeo, 1956, Contributo alla revisione dei Lumbricidae, Arch. Zool. Ital, 41, 129 Pop, 1941, Zur Phylogenie und Systematik der Lumbriciden, Zool. Jahrb. (Syst.), 74, 487 Blakemore, 2007, An updated list of valid, invalid and synonymous names of Criodriloidea and Lumbricoidea (Annelida: Oligochaeta: Criodrilidae, Sparganophilidae, Ailoscolecidae, Hormogastridae, Lumbricidae, Lutodrilidae), 1 Csuzdi, 2003 Qiu, 1998, Révision des taxons supraspécifiques de Lumbricoidea, Documents pedozoologiques et integrologiques, 3, 179 Mrsic, 1991, vol. 31 Sims, 1983, The scientific names of earthworms Gates, 1972, Burmese earthworms, Trans. Amer. Philosoph. Soc., 62, 1, 10.2307/1006214 Pop, 2005, An attempt to reconstruct the molecular phylogeny of the genus Allolobophora Eisen, 1874 (sensu lato, Pop, 1941) using 16S rDNA and COI sequences (Oligochaeta, Lumbricidae), 155 G. Eisen, Om Skandinaviens Lumbricider, Öfversigt Af Kongliga Vetenskaps-Akademiens Förhandligar 30 (1873) 43–56. Blakemore, 2008 Chang, 2009, Identifying earthworms through DNA barcodes: pitfalls and promise, Pedobiologia, 52, 171, 10.1016/j.pedobi.2008.08.002 King, 2008, Opening a can of worms: unprecedented sympatric cryptic diversity within British lumbricid earthworms, Mol. Ecol., 17, 4684, 10.1111/j.1365-294X.2008.03931.x Huang, 2007, Identifying earthworms through DNA barcodes, Pedobiologia, 51, 301, 10.1016/j.pedobi.2007.05.003 Cech, 2005, Remarks on the molecular phylogeny of the genus Dendrobaena (Sensu Pop, 1941) based on the investigation of 18S rDNA sequences, 155 Halanych, 2006, A review of molecular markers used for annelid phylogenetics, Integr. Comp. Biol., 46, 533, 10.1093/icb/icj052 Hebert, 2003, Biological identifications through DNA barcodes, P. Roy. Soc. London Ser. B. Biol. Sci., 270, 313, 10.1098/rspb.2002.2218 Savolainen, 2005, Towards writing the encyclopaedia of life: an introduction to DNA barcoding, Philos. T. Roy. Soc. B. Biol. Sci., 360, 1805, 10.1098/rstb.2005.1730 Richard, 2010, Re-integrating earthworm juveniles into soil biodiversity studies: species identification through DNA barcoding, Mol. Ecol. Resour., 10, 606, 10.1111/j.1755-0998.2009.02822.x Hajibabaei, 2007, DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics, Trends Genet., 23, 167, 10.1016/j.tig.2007.02.001 Avise, 2000 Avise, 2004 Valentini, 2009, DNA barcoding for ecologists, Trends Ecol. Evol., 24, 110, 10.1016/j.tree.2008.09.011 Pérez-Losada, 2005, Phylogenetic species delimitation of the earthworms Eisenia fetida (Savigny, 1826) and Eisenia andrei Bouché, 1972 (Oligochaeta, Lumbricidae) based on mitochondrial and nuclear DNA genes, Pedobiologia, 49, 317, 10.1016/j.pedobi.2005.02.004 Pop, 2008, Molecular taxonomy and phylogeny of the genera Octolasion Örley, 1885, Octodrilus Omodeo, 1856 and Octodriloides Zicsi, 1986 (Oligochaeta, Lumbricidae) based on nucleotide sequences of mitochondrial 16S rDNA and COI genes, 109 Chang, 2008, Molecular systematics and phylogeography of the gigantic earthworms of the Metaphire formosae species group (Clitellata, Megascolecidae), Mol. Phylogenet. Evol., 49, 958, 10.1016/j.ympev.2008.08.025 Chang, 2005, Taxonomic status and intraspecific phylogeography of two sibling species of Metaphire (Oligochaeta: Megascolecidae) in Taiwan, Pedobiologia, 49, 591, 10.1016/j.pedobi.2005.07.002 Minamiya, 2009, A phylogeographic study of the Japanese earthworm, Metaphire Sieboldi (Horst, 1883) (Oligochaeta: Megascolecidae): Inferences from mitochondrial DNA sequences, Eur. J. Soil Biol., 45, 423, 10.1016/j.ejsobi.2009.06.004 Novo, 2009, High genetic divergence of hormogastrid earthworms (Annelida, Oligochaeta) in the central Iberian Peninsula: evolutionary and demographic implications, Zool. Scr, 38, 537, 10.1111/j.1463-6409.2009.00389.x Rougerie, 2009, DNA barcodes for soil animal taxonomy, Pesqui. Agropecu. Bras, 44, 789, 10.1590/S0100-204X2009000800002 Novo, 2010, Cryptic speciation of hormogastrid earthworms revealed by mitochondrial and nuclear data, Mol. Phylogenet. Evol., 56, 507, 10.1016/j.ympev.2010.04.010 Folmer, 1994, DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates, Mol. Mar. Biol. Biotech., 3, 294 Katoh, 2005, MAFFT version 5: improvement in accuracy of multiple sequence alignment, Nucleic Acids Res., 33, 511, 10.1093/nar/gki198 Stamatakis, 2006, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, 22, 2688, 10.1093/bioinformatics/btl446 Posada, 2009, Selection of models of DNA evolution with JModelTest, Methods Mol. Biol., 537, 93, 10.1007/978-1-59745-251-9_5 Felsenstein, 1985, Confidence limits on phylogenies: an approach using the bootstrap, Evolution, 39, 783, 10.2307/2408678 Ronquist, 2003, MrBayes 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, 19, 1572, 10.1093/bioinformatics/btg180 Shimodaira, 1999, Multiple comparisons of log-likelihoods with applications to phylogenetic inference, Mol. Biol. Evol., 16, 1114, 10.1093/oxfordjournals.molbev.a026201 Huelsenbeck, 2002, Potential applications and pitfalls of Bayesian inference of phylogeny, Syst. Biol., 51, 673, 10.1080/10635150290102366 Easton, 1983, A guide to the valid names of Lumbricidae (Oligochaeta), 475 2004 Admassu, 2006, Earthworm primers for DNA-based gut content analysis and their cross-reactivity in a multi-species system, Soil Biol. Biochem., 38, 1308, 10.1016/j.soilbio.2005.08.019 Pop, 2007, Application of 16S, 18S rDNA and COI sequences in the molecular systematics of the earthworm family Lumbricidae (Annelida, Oligochaeta), Eur. J. Soil Biol., 43, 43, 10.1016/j.ejsobi.2007.08.007 Lund, 2009, Diversity and host specificity of the Verminephrobacter-earthworm symbiosis, Environ. Microbiol, 10.1111/j.1462-2920.2009.02084.x Leontieva, 2007, Phylogenetic analysis and identification of southeastern USA earthworm species in the genus Diplocardia using 16s rDNA and COI sequencing. Proceedings of ISEE8, Krakow 2006, Eur. J. Soil Biol., 43S Harris, 2003, Can you bank on GenBank?, Trends Ecol. Evol., 18, 317, 10.1016/S0169-5347(03)00150-2 Vilgalys, 2003, Taxonomic misidentification in public DNA databases, New Phytol., 160, 4, 10.1046/j.1469-8137.2003.00894.x Song, 2008, Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified, Proc. Natl. Acad. Sci. U S A, 105, 13486, 10.1073/pnas.0803076105 Buhay, 2009, COI-like" sequences are becoming problematic in molecular systematic and DNA barcoding studies, J. Crust. Biol., 29, 96, 10.1651/08-3020.1 Lopez, 1994, Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat, J. Mol. Evol., 39, 174, 10.1007/BF00163806