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References

  • Blaxter, M., Elsworth, B. & Daub, J. (2004) DNA taxonomy of a neglected animal phylum: an unexpected diversity of tardigrades. Proceedings of the Royal Society of London. Series B: Biological Sciences, 271, S189S192.
  • Blaxter, M., Mann, J., Chapman, T., Thomas, F., Whitton, C., Floyd, R. & Abebe, E. (2005) Defining operational taxonomic units using DNA barcode data. Philosophical Transactions of the Royal Society B: Biological Sciences, 360, 19351943.
  • Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K. & Madden, T. (2009) BLAST+: architecture and applications. BMC Bioinformatics, 10, 421.
  • Campbell, B.C., Steffen-Campbell, J.D. & Werren, J.H. (1993) Phylogeny of the Nasonia species complex (Hymenoptera: Pteromalidae) inferred from an internal transcribed spacer (ITS2) and 28S rDNA sequences. Insect Molecular Biology, 2, 225237.
  • Chang, F., Qiu, W., Zamar, R.H., Lazarus, R. & Wang, X. (2010) Clues: an R Package for nonparametric clustering based on local shrinking. Journal of Statistical Software, 33, 116.
  • Chesters, D. & Vogler, A.P. (2013) Resolving ambiguity of species limits and concatenation in multilocus sequence data for the construction of phylogenetic supermatrices. Systematic Biology, 62, 456466.
  • Cognato, A.I. (2006) Standard percent DNA sequence difference for insects does not predict species boundaries. Journal of Economic Entomology, 99, 10371045.
  • Edgar, R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 24602461.
  • Ence, D.D. & Carstens, B.C. (2011) SpedeSTEM: a rapid and accurate method for species delimitation. Molecular Ecology Resources, 11, 473480.
  • Ferguson, J.W.H. (2002) On the use of genetic divergence for identifying species. Biological Journal of the Linnean Society, 75, 509516.
  • Floyd, R., Abebe, E., Papert, A. & Blaxter, M. (2002) Molecular barcodes for soil nematode identification. Molecular Ecology, 11, 839850.
  • Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3, 294299.
  • Gillespie, J.J., Munro, J.B., Heraty, J.M., Yoder, M.J., Owen, A.K. & Carmichael, A.E. (2005) A secondary structural model of the 28S rRNA expansion segments D2 and D3 for chalcidoid wasps (Hymenoptera: Chalcidoidea). Molecular Biology and Evolution, 22, 15931608.
  • Göker, M., García-Blázquez, G., Voglmayr, H., Tellería, M.T. & Martín, M.P. (2009) Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora. PLoS ONE, 4, e6319.
  • Hebert, P.D.N., Ratnasingham, S. & DeWaard, J.R. (2003) Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London. Series B: Biological Sciences, 270, S596S599.
  • Hebert, P.D.N., Stoeckle, M.Y., Zemlak, T.S. & Francis, C.M. (2004) Identification of birds through DNA barcodes. PLoS Biology, 2, e312.
  • Heled, J. & Drummond, A.J. (2010) Bayesian inference of species trees from multi locus data. Molecular Biology and Evolution, 27, 570580.
  • Heraty, J.M., Hawks, D., Kostecki, J.S. & Carmichael, A. (2004) Phylogeny and behavior of the Gollumiellinae, a new subfamily of the ant parasitic Eucharitidae (Hymenoptera: Chalcidoidea). Systematic Entomology, 29, 544559.
  • Hibbett, D.S., Ohman, A., Glotzer, D., Nuhn, M., Kirk, P. & Nilsson, R.H. (2011) Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences. Fungal Biology Reviews, 25, 3847.
  • Hubert, L. & Arabie, P. (1985) Comparing partitions. Journal of Classification, 2, 193218.
  • Hugenholtz, P., Goebel, B.M. & Pace, N.R. (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. Journal of Bacteriology, 180, 47654774.
  • Knowles, L.L. & Carstens, B.C. (2007) Delimiting species without monophyletic gene trees. Systematic Biology, 56, 887895.
  • Koulianos, S. (1999) Phylogenetic relationship of the bumblebee subgenus Pyrobombus (Hymenoptera: Apidae) inferred from mitochondrial cytochromeb and cytochrome oxidase I sequence. Annals of the Entomological Society of America, 92, 355358.
  • Li, W., Jaroszewski, L. & Godzik, A. (2001) Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics, 17, 282283.
  • Lim, G.S., Balke, M. & Meier, R. (2012) Determining species boundaries in a world full of rarity: singletons, species delimitation methods. Systematic biology, 61, 165169.
  • Liu, L., Pearl, D.K., Brumfield, R.T. & Edwards, S.V. (2008) Estimating species trees using multiple-allele DNA sequence data. Evolution, 62, 20802091.
  • Mathog, D.R. (2003) Parallel BLAST on split databases. Bioinformatics, 19, 18651866.
  • 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. Systematic Biology, 57, 809813.
  • Meier, R., Shiyang, K., Vaidya, G. & Ng, P.K.L. (2006) DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Systematic Biology, 55, 715728.
  • Nilsson, R., Ryberg, M., Abarenkov, K., Sjokvist, E. & Kristiansson, E. (2009) The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiology Letters, 296, 97101.
  • O'Brien, H.E., Parrent, J.L., Jackson, J.A., Moncalvo, J.-M. & Vilgalys, R. (2005) Fungal community analysis by large-scale sequencing of environmental samples. Applied and Environmental Microbiology, 71, 55445550.
  • O'Meara, B.C. (2010) New heuristic methods for joint species delimitation and species tree inference. Systematic Biology, 59, 5973.
  • Osman, I.H. & Kelly, J.P. (Eds) (1996) Meta-Heuristics: Theory and Applications. Springer, Kluwer Academic Publishers, Norwell MA, USA.
  • Pons, J., Barraclough, T.G., Gomez-Zurita, J., Cardoso, A., Duran, D.P., Hazell, S., Kamoun, S., Sumlin, W.D. & Vogler, A.P. (2006) Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology, 55, 595609.
  • Powell, J.R., Monaghan, M.T., Opik, M. & Rillig, M.C. (2011) Evolutionary criteria outperform operational approaches in producing ecologically relevant fungal species inventories. Molecular Ecology, 20, 655666.
  • R Development Core Team (2008) R: A Language and Environment for Statistical Computing [Computer Software and Manual]. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org
  • Rattei, T., Tischler, P., Götz, S., Jehl, M.A., Hoser, J., Arnold, R., Conesa, A. & Mewes, H.W. (2010) SIMAP—a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters. Nucleic acids research, 38, D223D226.
  • Sauer, J. & Hausdorf, B. (2012) A comparison of DNA-based methods for delimiting species in a Cretan land snail radiation reveals shortcomings of exclusively molecular taxonomy. Cladistics, 28, 300316.
  • Schloss, P.D. & Handelsman, J. (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Applied and environmental microbiology, 71, 15011506.
  • Setaro, S.D., Garnica, S., Herrera, P.I., Suárez, J.P. & Göker, M. (2012) A clustering optimization strategy to estimate species richness of Sebacinales in the tropical Andes based on molecular sequences from distinct DNA regions. Biodiversity and Conservation, 21, 22692285.
  • Stackebrandt, E. & Goebel, B.M. (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. International Journal of Systematic Bacteriology, 44, 846849.
  • Sun, Y., Cai, Y., Liu, L., Yu, F., Farrell, M.L., McKendree, W. & Farmerie, W. (2009) ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Research, 37, e76.
  • Vogler, A.P. & Monaghan, M.T. (2006) Recent advances in DNA taxonomy. Journal of Zoological Systematics and Evolutionary Research, 45, 110.
  • Yang, Z. & Rannala, B. (2010) Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences of the United States of America, 107, 92649269.