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

Zobrazit více v PubMed

Barber KE, Mkoji GM, Loker ES. (2000) PCR-RFLP analysis of the ITS2 region to identify Schistosoma haematobium and S. bovis from Kenya. American Journal of Tropical Medicine and Hygiene 62: 434–440. www.ajtmh.org/content/62/4/434 PubMed

Besansky NJ, Severson DW, Ferdig MT. (2003) DNA barcoding of parasites and invertebrate disease vectors: what you don’t know can hurt you. Trends in Parasitology 19: 545-546. doi: 10.1016/j.pt.2003.09.015 PubMed DOI

Brant SV, Loker ES. (2009) Molecular systematic of the avian schistosome genus Trichobilharzia (Trematoda: Schistosomatidae) in North America. Journal of Parasitology 95: 941-63. doi: 10.1645/GE-1870.1 PubMed DOI PMC

Breman FC, Jordaens K, Sonet G, Nagy ZT, Van Houdt J, Louette M. (2013) DNA barcoding and evolutionary relationships in Accipiter Brisso, 1760 (Aves, Falconiformes: Accipitridae) with a focus on African and Eurasian representatives. Journal of Ornithology 154: 265-287. doi: 10.1007/s10336-012-0892-5 DOI

Brooks DR, Hoberg EP. (2001) Parasite systematics in the 21st century: opportunities and obstacles. Trends in Parasitology 17: 273-275. doi: 10.1016/S1471-4922(01)01894-3 PubMed DOI

Bueno Silva M. (2011) Cofilogeografia: estruturação geográfica, demografia histórica e associação entre species de Gyrodactylus (Monogenoidea: Gyrodactylidae) e hospedeiros Scleromystax (Siluriformes: Callichthyidae). PhD thesis, Universidade Federal do Paraná, Curitiba, Brazil.

Casu M, Lai T, Sanna D, Cossu P, Curini-Galletti M. (2009) An integrative approach to the taxonomy of the pigmented European Pseudomonocelis Meixner, 1943 (Platyhelminthes: Proseriata). Biological Journal of the Linnean Society 98: 907-922. doi: 10.1111/j.1095-8312.2009.01316.x DOI

Collins RA, Cruickshank RH. (2013) The seven deadly sins of DNA barcoding. Molecular Ecology Resources 13: 969-975. doi: 10.1111/1755-0998.12046 PubMed DOI

Cunningham CO. (1997) Species variation within the internal transcribed spacer (ITS) region of Gyrodactylus (Monogenea: Gyrodactylidae) ribosomal RNA genes. Journal of Parasitology 83: 215–219. http://www.jstor.org/stable/3284442, doi: 10.2307/3284442 PubMed DOI

Derycke S, Vanaverbeke J, Rigaux A, Backeljau T, Moens T. (2010) Exploring the use of cytochrome oxidase c subunit 1 (COI) for DNA barcoding of free-living marine nematodes. PLoS ONE 5: e13716. doi: 10.1371/journal.pone.0013716 PubMed DOI PMC

Desdevises Y, Jovelin R, Jousson O, Morand S. (2000) Comparison of ribosomal DNA sequences of Lamellodiscus spp. (Monogenea, Diplectanidae) parasitizing Pagellus (Sparidae, Teleostei) in the North Mediterranean Sea: species divergence and coevolutionary interactions. International Journal for Parasitology 30: 741-746. doi: 10.1016/S0020-7519(00)00051-5 PubMed DOI

Elsasser SC, Floyd R, Hebert PDN, Schulte-Hostedde AI. (2009) Species identification of North American guinea worms (Nematoda: Dracunculus) with DNA barcoding. Molecular Ecology Resources 9: 707-712. doi: 10.1111/j.1755-0998.2008.02393.x PubMed DOI

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: 294-299. PubMed

Fonseca VG, Carvalho GR, Sung W, Johnson HF, Power DM, Neill SP, Packer M, Blaxter ML, Lambshead PJD, Thomas WK, Creer S. (2010) Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nature Communications 1: 98. doi: 10.1038/ncomms1095 PubMed DOI PMC

García-Vásquez A, Hansen H, Shinn AP. (2007) A revised description of Gyrodactylus cichlidarum Paperna, 1968 (Gyrodactylidae) from the Nile tilapia, Oreochromis niloticus niloticus (Cichlidae), and its synonymy with G. niloticus Cone, Arthur et Bondad-Reantaso, 1995. Folia Parasitologica 54: 129–140. http://hdl.handle.net/1893/10236, http://folia.paru.cas.cz/detail.php?id=20841 PubMed

García-Vásquez A, Hansen H, Christison KW, Bron JE, Shinn AP. (2011) Description of three new species of Gyrodactylus von Nordmann, 1832 (Monogenea) parasitizing Oreochromis niloticus niloticus (L.) and O. mossambicus (Peters) (Cichlidae). Acta Parasitologica 56: 20–33. doi: 10.2478/s11686-011-0005-2 DOI

Gaunt MW, Miles MA. (2002) An insect molecular clock dates the origin of the insects and accords with palaeontological and biogeographic landmarks. Molecular Biology and Evolution 19: 748–761. http://mbe.oxfordjournals.org/content/19/5/748 PubMed

Gilmore SR, Cone DK, Lowe G, King SF, Jones SRM, Abbott CL. (2012) Molecular phylogeny of Gyrodactylus (Monogenea) parasitizing fishes in fresh water, estuarine, and marine habitats in Canada. Canadian Journal of Zoology 90: 776-786. doi: 10.1139/z2012-040 DOI

Hansen H, Bakke TA, Bachmann L. (2007) DNA taxonomy and barcoding of monogenean parasites: lessons from Gyrodactylus. Trends in Parasitology 23: 363-367. doi: 10.1016/j.pt.2007.06.007 PubMed DOI

Harris DJ, Crandall KA. (2000) Intragenomic variation within ITS1 and ITS2 of freshwater crayfishes (Decapoda: Cambaridae): implications for phylogenetic and microsatellite studies. Molecular Biology and Evolution 17: 284–291. http://mbe.oxfordjournals.org/content/17/2/284, doi: 10.1093/oxfordjournals.molbev.a026308 PubMed DOI

Hebert PDN, Cywinska A, Ball SL, de Waard JR. (2003a) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B 270: 313–322. doi: 10.1098/rspb.2002.2218 PubMed DOI PMC

Hebert PDN, Ratnasingham S, de Waard JR. (2003b) Barcoding animal life: cytochrome c oxidase subunit I divergences among closely related species. Proceedings of the Royal Society of London B 270: S96-S99. doi: 10.1098/rsbl.2003.0025 PubMed DOI PMC

Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM. (2004) Identification of birds through DNA barcodes. PLoS Biology 2: e312. doi: 10.1371/journal.pbio.0020312 PubMed DOI PMC

Hillis DM, Dixon MT. (1991) Ribosomal DNA: molecular evolution and phylogenetic inference. Quarterly Review of Biology 66: 411–453. http://www.jstor.org/stable/2831326, doi: 10.1086/417338 PubMed DOI

Hoberg EP. (1997) Phylogeny and historical reconstruction: host-parasite systems as keystones in biogeography and ecology. In: Reaka-Kudla ML, Wilson DE, Wilson EO. (Eds) Biodiversity II: understanding and protecting our biological resources. Joseph Henry Press, Washington, D.C.: 243-262.

Huyse T, Malmberg G. (2004) Molecular and morphological comparisons between Gyrodactylus ostendicus sp. nov. (Monogenea: Gyrodactylidae) on Pomatoschistus microps (Krøyer) and G. harengi Malmberg, 1957 on Clupea harengus membras L. Systematic Parasitology 58: 105-113. doi: 10.1023/B:SYPA.0000029423.68703.43 PubMed DOI

Huyse T, Pampoulie C, Audenaert V, Volckaert FAM. (2006) First report of Gyrodactylus spp. (Platyhelminthes: Monogenea) in the western Mediterranean sea: molecular and morphological descriptions. Journal of Parasitology 92: 682-690. doi: 10.1645/GE-690R.1 PubMed DOI

Huyse T, Plaisance L, Webster BL, Mo TA, Bakke TA, Bachmann L, Littlewood DTJ. (2007) The mitochondrial genome of Gyrodactylus salaris (Platyhelminthes: Monogenea), a pathogen of Atlantic salmon (Salmo salar). Parasitology 134: 739-747. doi: 10.1017/S0031182006002010 PubMed DOI

Huyse T, Buchmann K, Littlewood DTJ. (2008) The mitochondrial genome of Gyrodactylus derjavinoides (Platyhelminthes: Monogenea) – a mitogenomic approach for Gyrodactylus species and strain identification. Gene 417: 27-34. doi: 10.1016/j.gene.2008.03.008 PubMed DOI

Jörger KM, Schrödl M. (2013) How to describe a cryptic species? Practical challenges of molecular taxonomy. Frontiers in Zoology 10: 59. doi: 10.1186/1742-9994-10-59 PubMed DOI PMC

Jovelin R, Justine J-L. (2001) Phylogenetic relationships within the polyopisthocotylean monogeneans (Platyhelminthes) inferred from partial 28S rDNA sequences. International Journal for Parasitology 31: 393-401. doi: 10.1016/S0020-7519(01)00114-X PubMed DOI

Kang S, Kim J, Lee J, Kim S, Min G-S, Park J-K. (2012) The complete mitochondrial genome of an ectoparasitic monopisthocotylean fluke Benedenia hoshinai (Monogenea: Platyhelminthes). Mitochondrial DNA 23: 176-178. doi: 10.3109/19401736.2011.588223 PubMed DOI

Kimura M. (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111-120. doi: 10.1007/BF01731581 PubMed DOI

Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948. doi: 10.1093/bioinformatics/btm404 PubMed DOI

Larsson K, Ahmadzadeh A, Jondelius U. (2008) DNA taxonomy of Swedish Catenulida (Platyhelminthes) and a phylogenetic framework for catenulid classification. Organisms, Diversity & Evolution 8: 399-412. doi: 10.1016/j.ode.2008.09.003 DOI

Lázaro EM, Sluys R, Pala M, Angela Stocchino G, Baguñà J, Riutort M. (2009) Molecular barcoding and phylogeography of sexual and asexual freshwater planarians of the genus Dugesia in the Western Mediterranean (Platyhelminthes, Tricladida, Dugesiidae). Molecular Phylogenetics and Evolution 52: 835-845. doi: 10.1016/j.ympev.2009.04.022 PubMed DOI

Lefébure T, Douady CJ, Gouy M, Gilbert 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. doi: 10.1016/j.ympev.2006.03.014 PubMed DOI

Leung TLF, Donald KM, Keeney DB, Koehler AV, Peoples RC, Poulin R. (2009) Trematode parasites of Otago Harbour (New Zealand) soft-sediment intertidal ecosystems: life cycles, ecological roles and DNA barcodes. New Zealand Journal of Marine and Freshwater Research 43: 857-865. doi: 10.1080/00288330909510044 DOI

Li M, Shi S-F, Brown CL, Yang T-B. (2011) Phylogeographical pattern of Mazocraeoides gonialosae (Monogenea, Mazocraeidae) on the dotted gizzard shad, Konosirus punctatus, along the coast of China. International Journal for Parasitology 41: 1263-1272. doi: 10.1016/j.ijpara.2011.07.012 PubMed DOI

Littlewood DTJ. (2008) Platyhelminth systematics and the emergence of new characters. Parasite 15: 333-341. doi: 10.1051/parasite/2008153333 PubMed DOI

Littlewood DTJ, Rohde K, Clough KA. (1997) Parasite speciation within or between host species? Phylogenetic evidence from site-specific polystome monogeneans. International Journal for Parasitology 27: 1289-1297. doi: 10.1016/S0020-7519(97)00086-6 PubMed DOI

Locke SA, McLaughlin JD, Dayanandan S, Marcogliese DJ. (2010a) Diversity and specificity in Diplostomum spp. metacercariae in freshwater fishes revealed by cytochrome c oxidase I and internal transcribed spacer sequences. International Journal for Parasitology 40: 333-343. doi: 10.1016/j.ijpara.2009.08.012 PubMed DOI

Locke SA, McLaughlin JD, Marcogliese DJ. (2010b) DNA barcodes show cryptic diversity and a potential physiological basis for host specificity among Diplostomoidea (Platyhelminthes: Digenea) parasitizing freshwater fishes in the St. Lawrence River, Canada. Molecular Ecology 19: 2813-2827. doi: 10.1111/j.1365-294X.2010.04713.x PubMed DOI

Lockyer AE, Olson PD, Littlewood DTJ. (2003a) Utility of complete large and small subunit rRNA genes in resolving the phylogeny of the Neodermata (Platyhelminthes): implications and a review of the cercomer theory. Biological Journal of the Linnean Society 78: 155–171. doi: 10.1046/j.1095-8312.2003.00141.x DOI

Lockyer AE, Olson PD, Østergaard P, Rollinson D, Johnston DA, Attwood SW, Southgate VR, Horak P, Snyder SD, Le TH, Agatsuma T, McManus DP, Carmichael AC, Naem S, Littlewood DTJ. (2003b) The phylogeny of the Schistosomatidae based on three genes with emphasis on the interrelationships of Schistosoma Weinland, 1858. Parasitology 126: 203–224. doi: 10.1017/S0031182002002792 PubMed DOI

Lupi R, D’Onorio de Meo P, Picardi E, D’Antonio M, Paoletti D, Castrignanò T, Pesole G, Gissi C. (2010) MitoZoa: A curated mitochondrial genome database of metazoans for comparative genomics studies. Mitochondrion 10: 192-199. doi: 10.1016/j.mito.2010.01.004 PubMed DOI

Marcogliese DJ. (2004) Parasites: small players with crucial roles in the ecological theater. EcoHealth 1: 151-164. doi: 10.1007/s10393-004-0028-3 DOI

Matějusová I, Gelnar M, McBeath AJA, Collins CM, Cunningham CO. (2001) Molecular markers for gyrodactylids (Gyrodactylidae: Monogenea) from five fish families (Teleostei). International Journal for Parasitology 31: 738-745. doi: 10.1016/S0020-7519(01)00176-X PubMed DOI

McManus DP, Le TH, Blair D. (2004) Genomics of parasitic flatworms. International Journal for Parasitology 34: 153-158. doi: 10.1016/j.ijpara.2003.11.003 PubMed DOI

Meier R, Shiyang K, Vaidya G, Ng PKL. (2006) DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Systematic Biology 55: 715–728. doi: 10.1080/10635150600969864 PubMed DOI

Meinilä M, Kuusela J, Ziętara M, Lumme J. (2002) Primers for amplifying ~820 bp of highly polymorphic mitochondrial COI gene of Gyrodactylus salaris. Hereditas 137: 72-74. doi: 10.1034/j.1601-5223.2002.1370110.x PubMed DOI

Meusnier I, Singer GAC, Landry J-F, Hickey DA, Hebert PDN, Hajibabaei M. (2008) A universal DNA mini-barcode for biodiversity analysis. BMC Genomics 9: 214. doi: 10.1186/1471-2164-9-214 PubMed DOI PMC

Mladineo I, Šegvić T, Grubišić L. (2009) Molecular evidence for the lack of transmission of the monogenean Sparicotyle chrysophrii (Monogenea, Polyopisthocotylea) and isopod Ceratothoa oestroides (Crustacea, Cymothoidae) between wild bogue (Boops boops) and cage-reared sea bream (Sparus aurata) and sea bass (Dicentrarchus labrax). Aquaculture 295: 160-167. doi: 10.1016/j.aquaculture.2009.07.017 DOI

Mladineo I, Šegvić-Bubić T, Stanić R, Desdevises Y. (2013) Morphological plasticity and phylogeny in a monogenean parasite transferring between wild and reared fish populations. PLoS ONE 8: e62011. doi: 10.1371/journal.pone.0062011 PubMed DOI PMC

Moritz C, Cicero C. (2004) DNA barcoding: promise and pitfalls. PLoS Biology 2: e354. doi: 10.1371/journal.pbio.0020354 PubMed DOI PMC

Moszczynska A, Locke SA, McLaughlin JD, Marcogliese DJ, Crease TJ. (2009) Development of primers for the mitochondrial cytochrome c oxidase I gene in digenetic trematodes (Platyhelminthes) illustrates the challenge of barcoding parasitic helminths. Molecular Ecology Resources 9: 75-82. doi: 10.1111/j.1755-0998.2009.02634.x PubMed DOI

Nadler SA, Pérez-Ponce de Léon G. (2011) Integrating molecular and morphological approaches for characterizing parasite cryptic species: implications for parasitology. Parasitology 138: 1688-1709. doi: 10.1017/S003118201000168X PubMed DOI

Nieto Feliner G, Rosselló JA. (2007) Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Molecular Phylogenetics and Evolution 44: 911-919. doi: 10.1016/j.ympev.2007.01.013 PubMed DOI

Nolan MJ, Cribb TH. (2005) The use and implications of ribosomal DNA sequencing for the discrimination of digenean species. Advances in Parasitology 60: 101-163. doi: 10.1016/S0065-308X(05)60002-4 PubMed DOI

Odorico DM, Miller DJ. (1997) Variation in the ribosomal internal transcribed spacers and 5.8 s rDNA among five species of Acropora (Cnidaria; Scleractinia): patterns of variation consistent with reticulate evolution. Molecular Biology and Evolution 14: 465–473. http://mbe.oxfordjournals.org/content/14/5/465 PubMed

Olson PD, Littlewood DTJ. (2002) Phylogenetics of the Monogenea – evidence from a medley of molecules. International Journal for Parasitology 32: 233-244. doi: 10.1016/S0020-7519(01)00328-9 PubMed DOI

Paetow L, Cone D, Huyse T, McLaughlin J, Marcogliese D. (2009) Morphology and molecular taxonomy of Gyrodactylus jennyae n. sp (Monogenea) from tadpoles of captive Rana catesbeiana Shaw (Anura), with a review of the species of Gyrodactylus Nordmann, 1832 parasitising amphibians. Systematic Parasitology 73: 219-227. doi: 10.1007/s11230-009-9183-9 PubMed DOI

Paladini G, Cable J, Fioravanti ML, Faria PJ, Di Cave D, Shinn AP. (2009) Gyrodactylus orecchiae sp. n. (Monogenea: Gyrodactylidae) from farmed populations of gilthead seabream (Sparus aurata) in the Adriatic Sea. Folia Parasitologica 56: 21–28. http://hdl.handle.net/1893/1419, http://folia.paru.cas.cz/detail.php?id=21138 PubMed

Paladini G, Cable J, Fioravanti ML, Faria PJ, Shinn AP. (2010) The description of Gyrodactylus corleonis sp. n. and G. neretum sp. n. (Platyhelminthes: Monogenea) with comments on other gyrodactylids parasitising pipefish (Pisces: Syngnathidae). Folia Parasitologica 57: 17–30. http://hdl.handle.net/1893/9998, http://folia.paru.cas.cz/detail.php?id=21368 PubMed

Paladini G, Hansen H, Fioravanti ML, Shinn AP. (2011a) Gyrodactylus longipes n. sp. (Monogenea: Gyrodactylidae) from farmed gilthead seabream (Sparus aurata L.) from the Mediterranean. Parasitology International 60: 410-418. doi: 10.1016/j.parint.2011.06.022 PubMed DOI

Paladini G, Huyse T, Shinn AP. (2011b) Gyrodactylus salinae n. sp. (Platyhelminthes: Monogenea) infecting the south European toothcarp Aphanius fasciatus (Valenciennes) (Teleostei, Cyprinodontidae) from a hypersaline environment in Italy. Parasites & Vectors 4: 100. doi: 10.1186/1756-3305-4-100 PubMed DOI PMC

Palesse S, Meadors WA, de Buron I, Roumillat WA, Strand AE. (2011) Use of molecular tools in identification of philometrid larvae in fishes: technical limitations parallel our poor assessment of their biodiversity. Parasitology Research 109: 1725-1730. doi: 10.1007/s00436-011-2481-6 PubMed DOI

Park J-K, Kim K-H, Kang S, Kim W, Eom KS, Littlewood DTJ. (2007) A common origin of complex life cycles in parasitic flatworms: evidence from the complete mitochondrial genome of Microcotyle sebastis (Monogenea: Platyhelminthes). BMC Evolutionary Biology 7: 11. doi: 10.1186/1471-2148-7-11 PubMed DOI PMC

Perkins EM, Donnellan SC, Bertozzi T, Whittington ID. (2010) Closing the mitochondrial circle on paraphyly of the Monogenea (Platyhelminthes) infers evolution in the diet of parasitic flatworms. International Journal for Parasitology 40: 1237-1245. doi: 10.1016/j.ijpara.2010.02.017 PubMed DOI

Plaisance L, Huyse T, Littlewood DTJ, Bakke TA, Bachmann L. (2007) The complete mitochondrial DNA sequence of the monogenean Gyrodactylus thymalli (Platyhelminthes: Monogenea), a parasite of grayling (Thymallus thymallus). Molecular and Biochemical Parasitology 154: 190-194. doi: 10.1016/j.molbiopara.2007.04.012 PubMed DOI

Plaisance L, Rousset V, Morand S, Littlewood DTJ. (2008) Colonization of pacific islands by parasites of low dispersal abilities: phylogeography of two monogenean species parasitizing butterflyfishes in the Indo-West Pacific Ocean. Journal of Biogeography 35: 76-87. doi: 10.1111/j.1365-2699.2007.01794.x DOI

Poisot T, Verneau O, Desdevises Y. (2011) Morphological and molecular evolution are not linked in Lamellodiscus (Plathyhelminthes, Monogenea). PLoS ONE 6: e26252. doi: 10.1371/journal.pone.0026252 PubMed DOI PMC

Pouyaud L, Desmarais E, Deveney M, Pariselle A. (2006) Phylogenetic relationships among monogenean gill parasites (Dactylogyridea, Ancyrocephalidae) infesting tilapiine hosts (Cichlidae): systematic and evolutionary implications. Molecular Phylogenetics and Evolution 38: 241-249. doi: 10.1016/j.ympev.2005.08.013 PubMed DOI

Přikrylová I, Matĕjusová I, Musilová N, Gelnar M. (2009a) Gyrodactylus species (Monogenea: Gyrodactylidae) on the cichlid fishes of Senegal, with the description of Gyrodactylus ergensi sp. nov. from Mango tilapia, Sarotherodon galilaeus L. (Teleostei: Cichlidae). Parasitology Research 106: 1-6. doi: 10.1007/s00436-009-1600-0 PubMed DOI

Přikrylová I, Matĕjusová I, Musilová N, Gelnar M, Harris PD. (2009b) A new gyrodactylid (Monogenea) genus on gray bichir, Polypterus senegalus (Polypteridae) from Senegal (West Africa). Journal of Parasitology 95: 555-560. doi: 10.1645/GE-1652.1 PubMed DOI

Přikrylová I, Blažek R, Vanhove MPM. (2012a) An overview of the Gyrodactylus (Monogenea: Gyrodactylidae) species parasitizing African catfishes, and their morphological and molecular diversity. Parasitology Research 110: 1185-1200. doi: 10.1007/s00436-011-2612-0 PubMed DOI

Přikrylová I, Blažek R, Gelnar M. (2012b) Gyrodactylus malalai sp. nov. (Monogenea: Gyrodactylidae) from Nile tilapia, Oreochromis niloticus (L.) and Redbelly tilapia, Tilapia zillii (Gervais) (Teleostei: Cichlidae) in the Lake Turkana, Kenya. Acta Parasitologica 57: 122–130. doi: 10.2478/s11686-012-0017-6 PubMed DOI

Přikrylová I, Vanhove MPM, Janssens SB, Billeter PA, Huyse T. (2013) Tiny worms from a mighty continent: high diversity and new phylogenetic lineages of African monogeneans. Molecular Phylogenetics and Evolution 67: 43-52. doi: 10.1016/j.ympev.2012.12.017 PubMed DOI

Pugachev ON, Gerasev PI, Gussev AV, Ergens R, Khotenowsky I. (2009) Guide to Monogenoidea of freshwater fish of Palaearctic and Amur Regions. Ledizione-Ledi Publishing, Milan, 564 pp.

R Core Team (2012) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna: http://www.R-project.org/

Radulovici AE, Archambault P, Dufresne F. (2010) DNA barcodes for marine biodiversity: moving fast forward? Diversity 2: 450–472. doi: 10.3390/d2040450 DOI

Řehulková E, Mendlová M, Šimková A. (2013) Two new species of Cichlidogyrus (Monogenea: Dactylogyridae) parasitizing the gills of African cichlid fishes (Perciformes) from Senegal: morphometric and molecular characterization. Parasitology Research 112: 1399-1410. doi: 10.1007/s00436-013-3291-9 PubMed DOI

Rokicka M, Lumme J, Ziętara MS. (2009) Two new Antarctic Gyrodactylus species (Monogenoidea): description and phylogenetic characterization. Journal of Parasitology 95: 1112-1119. doi: 10.1645/GE-2002.1 PubMed DOI

Sanna D, Lai T, Francalacci P, Curini-Galletti M, Casu M. (2009) Population structure of the Monocelis lineata (Proseriata, Monocelididae) species complex assessed by phylogenetic analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Genetics and Molecular Biology 32: 864-867. doi: 10.1590/S1415-47572009005000076 PubMed DOI PMC

Schelkle B, Paladini G, Shinn AP, King S, Johnson M, van Oosterhout C, Mohammed RS, Cable J. (2011) Ieredactylus rivuli gen. et sp. nov. (Monogenea, Gyrodactylidae) from Rivulus hartii (Cyprinodontiformes, Rivulidae) in Trinidad. Acta Parasitologica 56: 360-370. doi: 10.2478/s11686-011-0081-3 DOI

Schockaert ER. (1996) Turbellarians. In: Hall GS. (Ed) Methods for the examination of organismal diversity in soils and sediments. CAB International, Wallingford, 221-226.

Schoelinck C. (2012) Systématique évolutive des Diplectanidae (Plathelminthes, Monogenea) parasites des Mérous des récifs coralliens (Perciformes, Serranidae). PhD thesis, Université Pierre et Marie Curie, Paris, France.

Schoelinck C, Cruaud C, Justine J-L. (2012) Are all species of Pseudorhabdosynochus strictly host specific? A molecular study. Parasitology International 61: 356-359. doi: 10.1016/j.parint.2012.01.009 PubMed DOI

Sonnenberg R, Nolte AW, Tautz D. (2007) An evaluation of LSU D1-D2 sequences for their use in species identification. Frontiers in Zoology 4: 6. doi: 10.1186/1742-9994-4-6 PubMed DOI PMC

Stefani F, Aquaro G, Azzurro E, Colorni A, Galli P. (2012) Patterns of genetic variation of a Lessepsian parasite. Biological Invasions 14: 1725-1736. doi: 10.1007/s10530-012-0183-3 DOI

Stoeckle M. (2003) Taxonomy, DNA, and the bar code of life. BioScience 53: 796–797. http://www.jstor.org/stable/10.1641/0006-3568%282003%29053%5B0796%3ATDATBC%5D2.0.CO%3B2 DOI

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 2731-2739. doi: 10.1093/molbev/msr121 PubMed DOI PMC

Taylor HR, Harris WE. (2012) An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Molecular Ecology Resources 12: 377-388. doi: 10.1111/j.1755-0998.2012.03119.x PubMed DOI

Telford MJ, Herniou EA, Russell RB, Littlewood DTJ. (2000) Changes in mitochondrial genetic codes as phylogenetic characters: two examples from the flatworms. Proceedings of the National Academy of Sciences of the USA 97: 11359-11364. doi: 10.1073/pnas.97.21.11359 PubMed DOI PMC

Telford MJ, Lockyer AE, Cartwright-Finch C, Littlewood DTJ. (2003) Combined large and small subunit ribosomal RNA phylogenies support a basal position of the acoelomorph flatworms. Proceedings of the Royal Society of London B 270: 1077-1083. doi: 10.1098/rspb.2003.2342 PubMed DOI PMC

Vanhove MPM. (2012) Species flocks and parasite evolution. Towards a co-phylogenetic analysis of monogenean flatworms of cichlids and gobies. PhD thesis, KU Leuven, Leuven, Belgium.

Vanhove MPM, Kovačić M, Koutsikos NE, Zogaris S, Vardakas LE, Huyse T, Economou AN. (2011a) First record of a landlocked population of marine Millerigobius macrocephalus (Perciformes: Gobiidae): observations from a unique spring-fed karstic lake (Lake Vouliagmeni, Greece) and phylogenetic positioning. Zoologischer Anzeiger 250: 195-204. doi: 10.1016/j.jcz.2011.03.002 DOI

Vanhove MPM, Snoeks J, Volckaert FAM, Huyse T. (2011b) First description of monogenean parasites in Lake Tanganyika: the cichlid Simochromis diagramma (Teleostei, Cichlidae) harbours a high diversity of Gyrodactylus species (Platyhelminthes, Monogenea). Parasitology 138: 364–380 (erratum in 138: 403). doi: 10.1017/S0031182010001356 PubMed DOI

Vanhove MPM, Economou AN, Zogaris S, Larmuseau MHD, Giakoumi S, Kalogianni E, Volckaert FAM, Huyse T. (2012) Phylogenetics and biogeography of the Balkan “sand gobies” (Teleostei, Gobiidae): vulnerable species in need of taxonomic revision. Biological Journal of the Linnean Society 105: 73-91. doi: 10.1111/j.1095-8312.2011.01781.x DOI

Vanhove MPM, Economou AN, Zogaris S, Giakoumi S, Zanella D, Volckaert FAM, Huyse T. (2013) The Gyrodactylus (Monogenea, Gyrodactylidae) parasite fauna of freshwater sand gobies (Teleostei, Gobioidei) in their centre of endemism, with description of seven new species. Parasitology Research. doi: 10.1007/s00436-013-3693-8 PubMed DOI

Van Steenkiste N, Tessens B, Willems W, Backeljau T, Jondelius U, Artois T. (2013) A comprehensive molecular phylogeny of Dalytyphloplanida (Platyhelminthes: Rhabdocoela) reveals multiple escapes from the marine environment and origins of symbiotic relationships. PLoS ONE 8: e59917. doi: 10.1371/journal.pone.0059917 PubMed DOI PMC

Vaughan DB, Christison KW, Hansen H, Shinn AP. (2010) Gyrodactylus eyipayipi sp. n. (Monogenea: Gyrodactylidae) from Syngnathus acus (Syngnathidae) from South Africa. Folia Parasitologica 57: 11–15. http://hdl.handle.net/1893/9958, http://folia.paru.cas.cz/detail.php?id=21366 PubMed

Vilas R, Criscione CD, Blouin MS. (2005) A comparison between mitochondrial DNA and the ribosomal internal transcribed regions in prospecting for cryptic species of platyhelminth parasites. Parasitology 131: 839-846. doi: 10.1017/S0031182005008437 PubMed DOI

Virgilio M, Backeljau T, Nevado B, De Meyer M. (2010) Comparative performance of DNA barcoding across insect orders. BMC Bioinformatics 11: 206. doi: 10.1186/1471-2105-11-206 PubMed DOI PMC

Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. (2005) Barcoding Australia’s fish species. Philosophical Transactions of the Royal Society of London B, Biological Sciences 360: 1847-1857. doi: 10.1098/rstb.2005.1716 PubMed DOI PMC

Ward RD, Hanner R, Hebert PDN. (2009) The campaign to DNA barcode all fishes, FISH-BOL. Journal of Fish Biology 74: 329-356. doi: 10.1111/j.1095-8649.2008.02080.x PubMed DOI

White TJ, Bruns T, Lee S, Taylor J. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: White TJ. (Ed) PCR protocols: a guide to methods and applications. Academic Press, San Diego, 315-322.

Whittington ID. (1998) Diversity “down under”: monogeneans in the Antipodes (Australia) with a prediction of monogenean biodiversity worldwide. International Journal for Parasitology 28: 1481-1493. doi: 10.1016/S0020-7519(98)00064-2 PubMed DOI

Wiemers M, Fiedler K. (2007) Does the DNA barcoding gap exist? A case study in blue butterflies (Lepidoptera: Lycaenidae). Frontiers in Zoology 4: 8. doi: 10.1186/1742-9994-4-8 PubMed DOI PMC

Willems WR, Wallberg A, Jondelius U, Littlewood DTJ, Backeljau T, Schockaert ER, Artois TJ. (2006) Filling a gap in the phylogeny of flatworms: relationships within the Rhabdocoela (Platyhelminthes), inferred from 18S ribosomal DNA sequences. Zoologica Scripta 35: 1-17. doi: 10.1111/j.1463-6409.2005.00216.x DOI

Windsor DA. (1998) Most of the species on Earth are parasites. International Journal for Parasitology 28: 1939-1941. doi: 10.1016/S0020-7519(98)00153-2 PubMed DOI

Zhang J, Wu X, Xie M, Xu X, Li A. (2011) The mitochondrial genome of Polylabris halichoeres (Monogenea: Microcotylidae). Mitochondrial DNA 22: 3-5. doi: 10.3109/19401736.2011.588223 PubMed DOI

Zhang J, Wu X, Xie M, Li A. (2012) The complete mitochondrial genome of Pseudochauhanea macrorchis (Monogenea: Chauhaneidae) revealed a highly repetitive region and a gene rearrangement hot spot in Polyopisthocotylea. Molecular Biology Reports 39: 8115-8125. doi: 10.1007/s11033-012-1659-z PubMed DOI

Ziętara MS, Lumme J. (2002) Speciation by host-switching and adaptive radiation in a fish parasite genus Gyrodactylus (Monogenea, Gyrodactylidae). Evolution 56: 2445-2458. doi: 10.1111/j.0014-3820.2002.tb00170.x PubMed DOI

Ziętara MS, Lebedeva D, Muñoz G, Lumme J. (2012) A monogenean fish parasite, Gyrodactylus chileani n. sp., belonging to a novel marine species lineage found in the South-Eastern Pacific and the Mediterranean and North Seas. Systematic Parasitology 83: 159-167. doi: 10.1007/s11230-012-9379-2 PubMed DOI PMC

An insight into the functional genomics and species classification of Eudiplozoon nipponicum (Monogenea, Diplozoidae), a haematophagous parasite of the common carp Cyprinus carpio

Morphometric and genetic evidence for cryptic diversity in Gyrodactylus (Monogenea) infecting non-native European populations of Ameiurus nebulosus and A. melas

Gyrodactylus ginestrae n. sp. (Monogenea: Gyrodactylidae), a parasite of the big-scale sand smelt, Atherina boyeri Risso, 1810 (Actinopterygii: Atherinidae) from the Black Sea

Species of Characidotrema Paperna & Thurston, 1968 (Monogenea: Dactylogyridae) from fishes of the Alestidae (Characiformes) in Africa: new species, host-parasite associations and first insights into the phylogeny of the genus

The first next-generation sequencing approach to the mitochondrial phylogeny of African monogenean parasites (Platyhelminthes: Gyrodactylidae and Dactylogyridae)

Occurrence and effect of trematode metacercariae in two endangered killifishes from Greece

Reduced host-specificity in a parasite infecting non-littoral Lake Tanganyika cichlids evidenced by intraspecific morphological and genetic diversity