Some taxonomic groups are less amenable to mitochondrial DNA barcoding than others. Due to the paucity of molecular information of understudied groups and the huge molecular diversity within flatworms, primer design has been hampered. Indeed, all attempts to develop universal flatworm-specific COI markers have failed so far. We demonstrate how high molecular variability and contamination problems limit the possibilities for barcoding using standard COI-based protocols in flatworms. As a consequence, molecular identification methods often rely on other widely applicable markers. In the case of Monogenea, a very diverse group of platyhelminth parasites, and Rhabdocoela, representing one-fourth of all free-living flatworm taxa, this has led to a relatively high availability of nuclear ITS and 18S/28S rDNA sequences on GenBank. In a comparison of the effectiveness in species assignment we conclude that mitochondrial and nuclear ribosomal markers perform equally well. In case intraspecific information is needed, rDNA sequences can guide the selection of the appropriate (i.e. taxon-specific) COI primers if available.

Aquatic animal health Fisheries and Oceans Canada Moncton NB Canada

Department of Invertebrate Zoology Swedish Museum of Natural History Stockholm Sweden

Division of Parasites and Vectors Department of Life Sciences Natural History Museum London United Kingdom

Laboratory of Biodiversity and Evolutionary Genomics Department of Biology University of Leuven Leuven Belgium ; Department of Biology Royal Museum for Central Africa Tervuren Belgium

Laboratory of Biodiversity and Evolutionary Genomics Department of Biology University of Leuven Leuven Belgium ; Present address Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic

Research Group Zoology Biodiversity and Toxicology Centre for Environmental Sciences Hasselt University Diepenbeek Belgium

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