Marine Biodiversity

, Volume 45, Issue 3, pp 433–451 | Cite as

Guidelines for DNA taxonomy, with a focus on the meiofauna

  • Diego FontanetoEmail author
  • Jean-François Flot
  • Cuong Q. Tang


Describing biological diversity is a challenging endeavour, especially for the small, cryptic animals that make up the meiofauna. The field of DNA taxonomy, i.e., the use of DNA to delineate species boundaries, is rapidly growing and changing; herein we review the recent advances in the acquisition of DNA sequence data and the analytical tools for DNA-based species delimitation, with a focus on applications to the meiofauna. After providing general guidelines on the data collection and analysis steps (sampling design, sequencing, phasing of nuclear markers, and sequence alignment), we explain the rationale and usage of several widely used or promising methods developed for delineating species from single-locus data sets (distance-based DNA barcoding, automated barcode gap discovery, K/θ, generalized mixed Yule–coalescent models, Poisson tree process model, and haplowebs). As it is increasingly recognised that several loci are required to delineate species accurately, we then briefly outline multilocus species delimitation approaches (Structure, Structurama, Bayesian phylogenetics & phylogeography, SpedeSTEM, O’Meara’s heuristic search, and several newly published Bayesian approaches based on the multispecies coalescent).


ABGD BP&P Biodiversity COI Cryptic species GMYC Identification PTP 



We thank Daniela Zappilli for organising a workshop on meiofaunal studies in Brest and for inviting us to write this manuscript. We thank also Timothy G. Barraclough, William C. Birky Jr, Bryan Carstens, Simon Dellicour, Christophe Douady, Florian Malard, Nicolas Puillandre, Fabio Stoch, Ziheng Yang, and two anonymous reviewers for comments and suggestions. J.-F.F. is supported by the European Research Council (ERC-2012-AdG 322790).


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Copyright information

© Senckenberg Gesellschaft für Naturforschung and Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Diego Fontaneto
    • 1
    Email author
  • Jean-François Flot
    • 2
  • Cuong Q. Tang
    • 3
    • 4
  1. 1.National Research CouncilInstitute of Ecosystem StudyVerbania PallanzaItaly
  2. 2.Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
  3. 3.Department of Life SciencesImperial College LondonBerkshireUK
  4. 4.Department of Life SciencesThe Natural History MuseumLondonUK

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