CSIRO Publishing blank image blank image blank image blank imageBooksblank image blank image blank image blank imageJournalsblank image blank image blank image blank imageAbout Usblank image blank image blank image blank imageShopping Cartblank image blank image blank image You are here: Journals > Invertebrate Systematics   
Invertebrate Systematics
Journal Banner
  Systematics, Phylogeny and Biogeography
 
blank image Search
 
blank image blank image
blank image
 
  Advanced Search
   

Journal Home
About the Journal
Editorial Board
Contacts
Content
Current Issue
Just Accepted
All Issues
Special Issues
Sample Issue
For Authors
General Information
Notice to Authors
Submit Article
Open Access
For Referees
Referee Guidelines
Review Article
Annual Referee Index
For Subscribers
Subscription Prices
Customer Service
Print Publication Dates

blue arrow e-Alerts
blank image
Subscribe to our Email Alert or RSS feeds for the latest journal papers.

red arrow Connect with us
blank image
facebook   youtube

red arrow Supplementary Series
blank image
All volumes of the Australian Journal of Zoology Supplementary Series are online.

 

Article << Previous     |     Next >>   Contents Vol 27(1)

DNA barcoding and species delimitation: the Stylodrilus heringianus case (Annelida : Clitellata : Lumbriculidae)

Ainara Achurra A C and Christer Erséus B

A Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of the Basque Country, Box 644, Leioa, Spain.
B Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 35 Göteborg, Sweden.
C Corresponding author. Email: ainara.achurra@ehu.es

Invertebrate Systematics 27(1) 118-128 http://dx.doi.org/10.1071/IS12049
Submitted: 16 June 2012  Accepted: 22 November 2012   Published: 13 March 2013


 
PDF (525 KB) $40
 Export Citation
 Print
  
Abstract

Individuals of the aquatic oligochaete species Stylodrilus heringianus Claparède, 1862 were collected across a part of this species’ distribution range in Sweden, Estonia, Great Britain and Spain to test whether they represent a single metapopulation or several separately evolving lineages. Using sequences of the barcoding gene cytochrome c oxidase subunit I (COI) and two nuclear genes (internal transcribed spacer region and histone 3), three different approaches were conducted: pairwise distance-method, Bayesian inference and network analysis. Both the COI phylogeny and network analyses were concordant in recovering six haplotype clusters, which showed a maximum genetic distance of 7.7% (K2P) among each other. Nevertheless, nuclear genes failed to confirm any lineage separation, and we conclude that the sampled specimens all belong to the same species. A phylogeographic history with allopatric divergence and secondary contact is suggested to explain this intraspecific pattern of mitochondrial divergence and nuclear non-divergence. The study shows that a mitochondrial single-locus approach can be problematic for the accurate delimitation of species, and we emphasise the need for nuclear genes as supplementary markers, when taxonomic resolution is assessed with COI barcodes.



References

Ballard, J. W. O., and Kreitman, M. (1995). Is mitochondrial DNA a strictly neutral marker? Trends in Ecology & Evolution 10, 485–488.
CrossRef | CAS |

Bely, A. E., and Wray, G. A. (2004). Molecular phylogeny of naidid worms (Annelida: Clitellata) based on cytochrom oxidase I. Molecular Phylogenetics and Evolution 30, 50–63.
CrossRef | CAS |

Ben-David, T., Melamed, S., Gerson, U., and Morin, S. (2007). ITS2 sequences as barcodes for identifying and analyzing spider mites (Acari: Tetranychidae). Experimental & Applied Acarology 41, 169–181.
CrossRef | CAS |

Brown, W. M. (1983). Evolution of animal mitochondrial DNA. In ‘Evolution of Genes and Proteins’. (Eds M. Nei and R. K. Koehn.) pp. 62–88. (Sinauer: Sunderland, MA, USA.)

Brown, S., Rouse, G., Hutchings, P., and Colgan, D. (1999). Assessing the usefulness of histone H3, U2 snRNA and 28rDNA in analyses of polychaete relationships. Australian Journal of Zoology 47, 499–516.
CrossRef |

Burton, T. E., and Davie, P. J. F. (2007). A revision of the shovel-nosed lobsters of the genus Thenus (Crustacea: Decapoda: Scyllaridae), with descriptions of three new species. Zootaxa 1429, 1–38.

Clement, M., Posada, D., and Crandall, K. A. (2000). TCS: a computer program to estimate gene genealogies. Molecular Ecology 9, 1657–1659.
CrossRef | CAS |

Cook, D. G. (1967). Studies on the Lumbriculidae (Oligochaeta) in Britain. Journal of Zoology 153, 353–368.
CrossRef |

de Queiroz, K. (2007). Species concepts and species delimitation. Systematic Biology 56, 879–886.
CrossRef |

de Queiroz, K. (2011). Branches in the lines of descent: Charles Darwin and the evolution of the species concept. Biological Journal of the Linnean Society. Linnean Society of London 103, 19–35.
CrossRef |

DeSalle, R., Egan, M. G., and Siddall, M. (2005). The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philosophical Transactions of the Royal Society B. Biological Sciences 360, 1905–1916.
CrossRef | CAS |

De Wit, P., and Erséus, C. (2010). Genetic variation and phylogeny of Scandinavian species of Grania (Annelida: Clitellata: Enchytraeidae), with the discovery of a cryptic species. Journal of Zoological Systematics and Evolutionary Research 48, 285–293.

Dowling, D. K., Friberg, U., and Lindell, J. (2008). Evolutionary implications of non-neutral mitochondrial genetic variation. Trends in Ecology & Evolution 23, 546–554.
CrossRef |

Durand, J. D., Persat, H., and Bouvet, Y. (1999). Phylogeography and postglacial dispersion of the chub (Leuciscus cephalus) in Europe. Molecular Ecology 8, 989–997.
CrossRef | CAS |

Erséus, C., and Gustafsson, D. (2009). Cryptic speciation in clitellate model organisms. In ‘Annelids in Modern Biology’. (Ed. Dan Shain.) pp. 31–46. (John Wiley & Sons: Hoboken, NJ, USA.)

Evans, B. J., Carter, T. F., Tobias, M. L., Kelley, D. B., Hanner, R., and Tinsley, R. C. (2008). A new species of clawed frog (genus Xenopus) from the Itombwe Massif, Democratic Republic of the Congo: implications for DNA barcodes and biodiversity conservation. Zootaxa 1780, 55–68.

Ferguson, J. W. H. (2002). On the use of genetic divergence for identifying species. Biological Journal of the Linnean Society. Linnean Society of London 75, 509–516.
CrossRef |

Fernández, R., Bergmann, P., Almodóvar, A., Díaz Cosín, D. J., and Heethoff, M. (2011). Ultrastructural and molecular insights into three populations of Aporrectodea trapezoids (Dugés, 1828) (Oligochaeta, Lumbricidae) with different reproductive modes. Pedobiologia 54, 281–290.
CrossRef |

Folmer, O., Black, M., Hoeh, W., Lutz, R., and Vrijenhoek, R. (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3, 294–299.
| CAS |

Funk, D. J., and Omland, K. E. (2003). Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology Evolution and Systematics 34, 397–423.
CrossRef |

Gustafsson, D. R., Price, D. A., and Erséus, C. (2009). Genetic variation in the popular lab worm Lumbriculus variegatus (Annelida: Clitellata: Lumbriculidae) reveals cryptic speciation. Molecular Phylogenetics and Evolution 51, 182–189.
CrossRef | CAS |

Hajibabaei, M., Janzen, D. H., Burns, J. M., Hallwachs, W., and Herbert, P. D. N. (2006). DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences of the United States of America 103, 968–971.
CrossRef |

Hayashi, M., and Chiba, S. (2000). Intraspecific diversity of mitochondrial DNA in the land snail Euhadra peliomphala (Bradybaenidae). Biological Journal of the Linnean Society. Linnean Society of London 70, 391–401.
CrossRef |

Hebert, P. D. N. (2004). Identification of birds through DNA barcodes. PLoS Biology 2, e312.
CrossRef |

Hebert, P. D. N., and Gregory, T. R. (2005). The promise of DNA barcoding for taxonomy. Systematic Biology 54, 852–859.
CrossRef |

Hebert, P. D. N., Cywinska, A., Ball, S. L., and deWaard, J. R. (2003a). Biological identifications through DNA barcodes. Proceedings of the Royal Society B. Biological Sciences 270, 313–321.
CrossRef | CAS |

Hebert, P. D. N., Ratnasingham, S., and deWaard, J. R. (2003b). Barcoding animal life: cytochrome c oxidase subunit I divergences among closely related species. Proceedings of the Royal Society B. Biological Sciences 270, S96–S99.
CrossRef | CAS |

Hebert, P. D. N., Penton, E. H., Burns, J., Janzen, D. J., and Hallwachs, W. (2004). Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly, Astraptes fulgerator. Proceedings of the National Academy of Sciences of the United States of America 101, 14812–14817.
CrossRef | CAS |

Hewitt, G. M. (1996). Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society. Linnean Society of London 58, 247–276.

Hewitt, G. M. (1999). Post-glacial recolonization of European Biota. Biological Journal of the Linnean Society. Linnean Society of London 68, 87–112.
CrossRef |

Hickerson, M. J., Meyer, C. P., and Moritz, C. (2006). DNA barcoding will often fail to discover new animal species over broad parameter space. Systematic Biology 55, 729–739.
CrossRef |

Källersjö, M., Von Proschwitz, T., Lundberg, S., Eldenäs, P., and Erséus, C. (2005). Evaluation of ITS rDNA as a complement to mitochondrial gene sequences for phylogenetic studies in freshwater mussels: an example using Unionidae from north-western Europe. Zoologica Scripta 34, 415–424.
CrossRef |

Koski, L. B., and Golding, G. B. (2001). The closest BLAST hit is often not the nearest neighbor. Journal of Molecular Evolution 52, 540–542.
| CAS |

Kress, W. J., and Erickson, D. L. (2008). DNA barcodes: genes, genomics, and bioinformatics. Proceedings of the National Academy of Sciences of the United States of America 105, 2761–2762.
CrossRef | CAS |

Kvist, S., Sarkar, I. N., and Erséus, C. (2010). Genetic variation and phylogeny of the cosmopolitan marine genus Tubificoides (Annelida: Clitellata: Naididae: Tubificinae). Molecular Phylogenetics and Evolution 57, 687–702.
CrossRef | CAS |

Kwong, S., Srivathsan, A., and Meier, R. (2012). An update on DNA barcoding: low species coverage and numerous unidentified sequences. Cladistics 28, 639–644.
CrossRef |

Laakso, M. (1967). New records of aquatic Oligochaeta from Finland. Annales Zoologici Fennici 6, 348–352.

Lefébure, T., Douady, C. J., Gouy, M., and Gibert, J. (2006). Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation. Molecular Phylogenetics and Evolution 40, 435–447.
CrossRef |

Li, Y., Zhou, X., Feng, G., Hu, H., Niu, L., Hebert, P. D. N., and Huang, D. (2010). COI and ITS2 sequences delimit species, reveal cryptic taxa and host specificity of fig-associated Sycophila (Hymenoptera, Eurytomidae). Molecular Ecology Resources 10, 31–40.
CrossRef | CAS |

Lou, M., and Golding, G. B. (2012). The effect of sampling from subdivided populations on species identification with DNA barcodes using a Bayesian statistical approach. Molecular Phylogenetics and Evolution 65, 765–773.
CrossRef |

Martin, P. R., and McKay, J. K. (2004). Latitudinal variation in genetic divergence of populations and the potential for future speciation. Evolution 58, 938–945.

Meier, R. (2008). DNA sequences in taxonomy: opportunities and challenges. In ‘The New Taxonomy’. (Ed. Q. Wheeler.) (CRC Press: Boca Raton, FL, USA.)

Meier, R., Shiyang, K., Vaidya, G., and Ng, P. K. L. (2006). DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Systematic Biology 55, 715–728.
CrossRef |

Meier, R., Zhang, G. Y., and Ali, F. (2008). The use of mean instead of smallest interspecific distances exaggerates the size of the “Barcoding Gap” and leads to misidentification. Systematic Biology 57, 809–813.
CrossRef |

Milbrink, G. (1973). On the use of indicator communities of Tubificidae and some Lumbriculidae in the assessment of water pollution in Swedish lakes. Zoon 1, 125–139.

Moore, W. S. (1995). Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees. Evolution 49, 718–726.
CrossRef |

Moritz, C., and Cicero, C. (2004). DNA barcoding: promise and pitfalls. PLoS Biology 2, e354.
CrossRef |

Nygren, A., and Pleijel, F. (2011). From one to ten in a single stroke – resolving the European Eumidasanguinea (Phyllodocidae, Annelida) species complex. Molecular Phylogenetics and Evolution 58, 132–141.
CrossRef |

Nygren, A., Eklöf, J., and Pleijel, F. (2009). Arctic-boreal sibling species of Paranaitis. Marine Biology Research 5, 315–327.
CrossRef |

Nygren, A., Eklöf, J., and Pleijel, F. (2010). Cryptic species of Notophyllum (Polychaeta: Phyllodocidae) in Scandinavian waters. Organisms, Diversity & Evolution 10, 193–204.
CrossRef |

Nylander, J. A. A. (2004). MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University.

Posada, D., and Crandall, K. A. (2001). Intraspecific phylogenetics: trees grafting into networks. Trends in Ecology & Evolution 16, 37–45.
CrossRef |

Rambaut, A., and Drummond, A. J. (2009). Tracer v1.5. Available at http://beast.bio.ed.ac.uk/Tracer

Rodriguez, P. (1988). Sur certaines espèces de Lumbriculidae (Annelida: Oligochaeta) du nord de la péninsule ibérique. Annales de Limnologie 24, 203–211.
CrossRef |

Ronquist, F., and Huelsenbeck, J. P. (2003). MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574.
CrossRef | CAS |

Rubinoff, D., Cameron, S., and Will, K. (2006). A genomic perspective on the shortcomings of mitochondrial DNA for “barcoding” identification. The Journal of Heredity 97, 581–594.
CrossRef | CAS |

Srivathsan, A., and Meier, R. (2012). On the inappropriate use of Kimura-2-parameter (K2P) divergences in the DNA-barcoding literature. Cladistics 27, 1–15.

Stamatakis, A., Hoover, P., and Rougemont, J. (2008). A rapid bootstrap algorithm for the RAxML web-servers. Systematic Biology 57, 758–771.
CrossRef |

Steel, M. A., Hendy, M. D., and Penny, D. (1988). Loss of information in genetic distances. Nature 336, 118.
CrossRef | CAS |

Swofford, D. L. (2002). ‘PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods).’ (Sinauer Associates, Sunderland, MA, USA.)

Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25, 4876–4882.
CrossRef | CAS |

Verovnik, R., Sket, B., and Trontelj, P. (2005). The colonization of Europe by the freshwater crustacean Asellus aquaticus (Crustacea: Isopoda) proceeded from ancient refugia and was directed by habitat connectivity. Molecular Ecology 14, 4355–4369.
CrossRef | CAS |

Vogler, A. P., and Monaghan, M. T. (2007). Recent advances in DNA taxonomy. Journal of Zoological Systematics and Evolutionary Research 45, 1–10.
CrossRef |

White, T. J., Bruns, T., Lee, S., and Taylor, J. W. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In ‘PCR Protocols: A Guide to Methods and Applications’. (Eds M. A. Innis, D. H. Gelfand, J. J. Sninsky and T. J. White.) pp. 315–322. (Academic Press: New York.)

Whitworth, T. L., Dawson, R. D., Magalon, H., and Baudry, E. (2007). DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae). Proceedings. Biological Sciences 274, 1731–1739.
CrossRef | CAS |

Will, K. W., and Rubinoff, D. (2004). Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics 20, 47–55.
CrossRef |

Will, K. W., Mishler, B., and Wheeler, Q. (2005). The perils of DNA barcoding and the need for integrative taxonomy. Systematic Biology 54, 844–851.
CrossRef |

Yao, H., Song, J., Liu, C., Luo, K., Han, J., Li, Y., Pang, X., Xu, H., Zhu, Y., Xiao, P., and Chen, S. (2010). Use of ITS2 region as the universal DNA barcode for plants and animals. PLoS ONE 5, e13102.
CrossRef |

Zhou, H., Fend, S. V., Gustafson, D. L., De Wit, P., and Erséus, C. (2010). Molecular phylogeny of Nearctic species of Rhynchelmis (Annelida). Zoologica Scripta 39, 378–393.
CrossRef |


   
Subscriber Login
Username:
Password:  

 
    
Legal & Privacy | Contact Us | Help

CSIRO

© CSIRO 1996-2013