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Mitochondrial DNA Part A
DNA Mapping, Sequencing, and Analysis
Volume 27, 2016 - Issue 3
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Full Length Research Paper

Does a global DNA barcoding gap exist in Annelida?

Pages 2241-2252 | Received 02 Oct 2014, Accepted 01 Nov 2014, Published online: 28 Nov 2014

References

  • Bely AE, Weisblat DA. (2006). Lessons from leeches: A call for DNA barcoding in the lab. Evol Dev 8:491–501
  • Blakemore RJ. (2006). Cosmopolitan earthworms – An eco-taxonomic guide to the peregrine species of the world. Kippax, Australia: VermEcology
  • Bleidorn C, Vogt L, Bartolomaeus T. (2003). New insights into polychaete phylogeny (Annelida) inferred from 18S rDNA sequences. Mol Phyl Evol 29:279–88
  • Burns JM, Janzen DH, Hajibabaei M, Hallwachs W, Hebert PDN. (2007). DNA barcodes of closely related (but morphologically and ecologically distinct) species of skipper butterflies (Hesperiidae) can differ by only one to three nucleotides. J Lepid Soc 61:138–53
  • Carr CM, Hardy SM, Brown TM, Macdonald TA, Hebert PD. (2011). A tri-oceanic perspective: DNA barcoding reveals geographic structure and cryptic diversity in Canadian polychaetes. PLoS One 6:e22232
  • Chang CH, Rougerie R, Chen JH. (2009). Identifying earthworms through DNA barcodes: Pitfalls and promise. Pedobiologia 52:171–80
  • Chapple DG, Ritchie PA. (2013). A retrospective approach to testing the DNA barcoding method. PLoS One 8:e77882
  • Collins RA, Cruickshank RH. (2013). The seven deadly sins of DNA barcoding. Mol Ecol Res 13:969–75
  • DasGupta B, Konwar KM, Măndoiu II, Shvartsman AA. (2005). DNA-BAR: Distinguisher selection for DNA barcoding. Bioinformatics 21:3424–6
  • Decaëns T, Porco D, Rougerie R, Brown GG, James SW. (2013). Potential of DNA barcoding for earthworm research in taxonomy and ecology. Appl Soil Ecol 65:35–42
  • DeSalle R, Egan MG, Siddall M. (2005). The unholy trinity: Taxonomy, species delimitation and DNA barcoding. Philos T Roy Soc B 360:1905–16
  • De Wit P, Erséus C. (2010). Genetic variation and phylogeny of Scandinavian species of Grania (Annelida: Clitellata: Enchytraeidae), with the discovery of a cryptic species. J Zool Syst Evol Res 48:285–93
  • Elias M, Hill RI, Willmott KR, Dasmahapatra KK, Brower AV, Mallet J, Jiggins CD. (2007). Limited performance of DNA barcoding in a diverse community of tropical butterflies. Proc R Soc Lond B 274:2881–9
  • Erséus C. (2005). Phylogeny of oligochaetous Clitellata. Hydrobiologia 535/536:357–72
  • Erséus C, Kvist S. (2007). COI variation in Scandinavian marine species of Tubificoides (Annelida: Clitellata: Tubificidae). J Mar Biol Assoc UK 87:1121–6
  • Fernández R, Almodóvar A, Novo M, Gutiérrez M, Díaz Cosín D. (2011). A vagrant clone in a peregrine species: Phylogeography, high clonal diversity and geographical distribution in the earthworm Aporrectodea trapezoides (Dugès, 1828). Soil Biol Biochem 43:2085–93
  • Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek RC. (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3:294–9
  • Hebert PDN, Cywinska A, Ball SL, deWaard JR. (2003a). Biological identifications through DNA barcodes. Proc R Soc Lond B 270:313–21
  • Hebert PD, Gregory TR. (2005). The promise of DNA barcoding for taxonomy. Syst Biol 54:852–9
  • Hebert PDN, Ratnasingham S, deWaard JR. (2003b). Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond B 270:S96–9
  • Heimeier D, Lavery S, Sewell MA. (2010). Using DNA barcoding and phylogenetics to identify Antarctic invertebrate larvae: Lessons from a large scale study. Mar Genomics 3:165–77
  • Huang J, Xu Q, Sun ZJ, Tang GL, Su ZY. (2007). Identifying earthworms through DNA barcodes. Pedobiologia 51:301–9
  • James SW, Porco D, Decaëns T, Richard B, Rougerie R, Erséus C. (2010). DNA barcoding reveals cryptic diversity in Lumbricus terrestris L., 1758 (Clitellata): Resurrection of L. herculeus (Savigny, 1826). PLoS One 5:e15629
  • Katoh K, Standley DM. (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol Biol Evol 30:772–80
  • Kvist S. (2013). Barcoding in the dark?: A critical view of the sufficiency of zoological DNA barcoding databases and a plea for broader integration of taxonomic knowledge. Mol Phylogenet Evol 69:39–45
  • Kvist S, Laumer C, Junoy J, Giribet G. (2014). A further contribution to the phylogeny, systematics and DNA barcoding of Nemertea. Invert Syst 28:287–308
  • Kvist S, Narechania A, Oceguera-Figueroa A, Fuks B, Siddall ME. (2011). Phylogenomics of Reichenowia parasitica, an alphaproteobacterial endosymbiont of the freshwater leech Placobdella parasitica. PLoS One 6:e28192
  • Kvist S, Oceguera-Figueroa A, Siddall ME, Erséus C. (2010). Barcoding, types and the Hirudo files: Using information content to critically evaluate the identity of DNA barcodes. Mitochondrial DNA 21:198–205
  • Kvist S, Siddall ME. (2013). Phylogenomics of Annelida revisited: A cladistic approach using genome-wide expressed sequence tag data mining and examining the effects of missing data. Cladistics 29:435–48
  • Little DP. (2011). DNA barcode sequence identification incorporating taxonomic hierarchy and within taxon variability. PLoS One 6:e20552
  • Luttikhuizen PC, Dekker R. (2010). Pseudo-cryptic species Arenicola defodiens and Arenicola marina (‘Polychaeta’: Arenicolidae) in Wadden Sea, North Sea and Skagerrak: Morphological and molecular variation. J Sea Res 63:17–23
  • Maddison WP, Maddison DR. (2010). Mesquite: A modular system for evolutionary analysis version 2.5. Available at: http://mesquiteproject.org (Accessed 12 July 2014)
  • Martinsson S, Achurra A, Svensson M, Erséus C. (2013). Integrative taxonomy of the freshwater worm Rhyacodrilus falciformis s.l. (Clitellata: Naididae), with the description of a new species. Zool Scr 42:612–22
  • Meier R, Shiyang K, Vaidya G, Ng PK. (2006). DNA barcoding and taxonomy in Diptera: A tale of high intraspecific variability and low identification success. Syst Biol 55:715–28
  • Meier R, Zhang G, Ali F. (2008). The use of mean instead of smallest interspecific distances exaggerates the size of the “barcoding gap” and leads to misidentification. Syst Biol 57:809–13
  • Meyer CP, Paulay G. (2005). DNA barcoding: Error rates based on comprehensive sampling. PLoS Biol 3:e422
  • Moritz C, Cicero C. (2004). DNA barcoding: Promise and pitfalls. PLoS Biol 2:1529–31
  • Novo M, Almodóvar A, Díaz-Cosín D. (2009). High genetic divergence of hormogastrid earthworms (Annelida, Oligochaeta) in the central Iberian Peninsula: Evolutionary and demographic implications. Zool Scr 38:537–52
  • Novo M, Almodóvar A, Fernández R, Trigo D, Díaz Cosín D. (2010). Cryptic speciation of hormogastrid earthworms revealed by mitochondrial and nuclear data. Mol Phylogenet Evol 56:507–12
  • Oceguera-Figueroa A, León-Règagnon V, Siddall ME. (2010). DNA barcoding reveals Mexican diversity within the freshwater leech genus Helobdella (Annelida: Glossiphoniidae). Mitochondrial DNA 21:24–9
  • Oceguera-Figueroa A, Phillips AJ, Pacheco-Chaves B, Reeves WK, Siddall ME. (2011). Phylogeny of macrophagous leeches (Hirudinea, Clitellata) based on molecular data and evaluation of the barcoding locus. Zool Scr 40:194–203
  • Pérez-Losada M, Bloch R, Breinholt JW, Pfenninger M, Domínguez J. (2012). Taxonomic assessment of Lumbricidae (Oligochaeta) earthworm genera using DNA barcodes. Eur J Soil Biol 48:41–7
  • Puillandre N, Lambert A, Brouillet S, Achaz G. (2012). ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Mol Ecol 21:1864–77
  • Richard B, Decaëns T, Rougerie R, James SW, Porco D, Hebert PDN. (2010). Re-integrating earthworm juveniles into soil biodiversity studies: Species identification through DNA barcoding. Mol Ecol Res 10:606–14
  • Rouse GW, Pleijel F. (2001). Polychaetes. New York, NY: Oxford University Press
  • Rousset V, Pleijel F, Rouse GW, Erséus C, Siddall ME. (2007). A molecular phylogeny of annelids. Cladistics 23:41–63
  • Sarkar IN, Planet PJ, Bael TE, Stanley SE, Siddall M, DeSalle R, Figurski DH. (2002). Characteristic attributes in cancer microarrays. J Biomed Inform 35:111–22
  • Schüller M. (2011). Evidence for a role of bathymetry and emergence in speciation in the genus Glycera (Glyceridae, ‘Polychaeta’) from the deep Eastern Weddell Sea. Polar Biol 34:549–64
  • Shain DH. (2009). Annelids in modern biology. New York, NY, USA: John Wiley and Sons
  • Siddall ME, Budinoff RB. (2005). DNA-barcoding evidence for widespread introductions of a leech from the South American Helobdella triserialis complex. Conserv Genet 6:467–72
  • Siddall ME, Fontanella FM, Watson SC, Kvist S, Erséus C. (2009). Barcoding bamboozled by bacteria: Convergence to metazoan mitochondrial primer targets by marine microbes. Syst Biol 58:445–51
  • Srivathsan A, Meier R. (2012). On the inappropriate use of Kimura-2-parameter (K2P) divergences in the DNA-barcoding literature. Cladistics 28:190–4
  • Stoeckle M. (2003). Taxonomy, DNA, and the bar code of life. BioScience 53:796–7
  • Stothard P. (2000). The Sequence Manipulation Suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 28:1102–4
  • Struck T, Hessling R, Purschke G. (2002). The phylogenetic position of the Aelosomatidae and Parergordrilidae, two enigmatic oligochaete-like taxa of the ‘Polychaeta’, based on molecular data from 18S rDNA sequences. J Zool Syst Evol Res 40:155–63
  • Struck TH, Paul C, Hill N, Hartmann S, Hösel C, Kube M, Lieb B, et al. (2011). Phylogenomic analyses unravel annelid evolution. Nature 471:95–8
  • Swofford DL. (2003). PAUP*. Phylogenetic analysis using parsimony (*and Other Methods). Version 4. Sunderland, MA, USA: Sinauer Associates
  • Trewick SA. (2008). DNA barcoding is not enough: Mismatch of taxonomy and genealogy in New Zealand grasshoppers (Orthoptera: Acrididae). Cladistics 24:240–54
  • Weigert A, Helm C, Meyer M, Nickel B, Arendt D, Hausdorf B, Santos SR, et al. (2014). Illuminating the base of the annelid tree using transcriptomics. Mol Biol Evol 31:1391–401
  • Weitschek E, Van Velzen R, Felici G, Bertolazzi P. (2013). BLOG 2.0: A software for character-based species classification with DNA barcode sequences. What it does, how to use it? Mol Ecol Res 13:1043–6
  • Wiemers M, Fiedler K. (2007). Does the DNA barcoding gap exist? – A case study in blue butterflies (Lepidoptera: Lycaenidae). Front Zool 4:1–16
  • Will KW, Rubinoff D. (2004). Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics 20:47–55
  • Zhang Z-Q. (2011). Animal biodiversity: An introduction to higher-level classification and taxonomic richness. Zootaxa 3148:7–12
  • Zhou H, Zhang Z, Chen H, Sun R, Wang H, Guo L, Pan H. (2010). Integrating a DNA barcoding project with an ecological survey: A case study on temperate intertidal polychaete communities in Qingdao, China. Chin J Oceanol Limnol 28:899–910

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