@article {6507, title = {DNA barcoding echinoderms from the East Coast of South Africa. The challenge to maintain DNA data connected with taxonomy}, journal = {PLoS ONE}, volume = {17}, year = {2022}, month = {Oct-10-2022}, pages = {e0270321}, abstract = {

Echinoderms are marine water invertebrates that are represented by more than 7000 extant species, grouped in five classes and showing diverse morphologies (starfish, sea lilies, feather stars, sea urchins, sea cucumbers, brittle and basket stars). In an effort to further study their diversity, DNA barcodes (DNA fragments of the 5\’ end of the cytochrome c oxidase subunit I gene, COI) have been used to complement morphological examination in identifying evolutionary lineages. Although divergent clusters of COI sequences were reported to generally match morphological species delineations, they also revealed some discrepancies, suggesting overlooked species, ecophenotypic variation or multiple COI lineages within one species. Here, we sequenced COI fragments of 312 shallow-water echinoderms of the East Coast of South Africa (KwaZulu-Natal Province) and compared morphological identifications with species delimitations obtained with four methods that are exclusively based on COI sequences. We identified a total of 103 morphospecies including 18 that did not exactly match described species. We also report 46 COI sequences that showed large divergences (\>5\% p-distances) with those available to date and publish the first COI sequences for 30 species. Our analyses also identified discordances between morphological identifications and COI-based species delimitations for a considerable proportion of the morphospecies studied here (49/103). For most of them, further investigation is necessary to keep a sound connection between taxonomy and the growing importance of DNA-based research.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0270321}, url = {http://dx.doi.org/10.1371/journal.pone.0270321}, author = {Sonet, Gontran and Smitz, Nathalie and Vangestel, Carl and Samyn, Yves}, editor = {Chiang, Tzen-Yuh} } @article {4686, title = {A genome-wide data assessment of the African lion (Panthera leo) population genetic structure and diversity in Tanzania}, journal = {PLOS ONE}, volume = {13}, year = {2018}, month = {Jul-11-2018}, pages = {e0205395}, doi = {10.1371/journal.pone.0205395}, url = {http://dx.plos.org/10.1371/journal.pone.0205395}, author = {Smitz, Nathalie and Jouvenet, Olivia and Ambwene Ligate, Fredrick and Crosmary, William-George and Ikanda, Dennis and Chardonnet, Philippe and Fusari, Alessandro and Meganck, Kenny and Gillet, Fran{\c c}ois and Melletti, Mario and Michaux, Johan R.}, editor = {Chiang, Tzen-Yuh} } @article {4623, title = {DNA barcoding to improve the taxonomy of the Afrotropical hoverflies (Insecta: Diptera: Syrphidae)}, journal = {PLOS ONE}, volume = {10}, year = {2015}, month = {Apr-10-2016}, pages = {e0140264}, doi = {10.1371/journal.pone.0140264}, url = {http://dx.plos.org/10.1371/journal.pone.0140264}, author = {Jordaens, Kurt and Goergen, Georg and Virgilio, Massimiliano and Backeljau, Thierry and Vokaer, Audrey and De Meyer, Marc}, editor = {Casiraghi, Maurizio} } @article {4437, title = {Taxonomic Identity of the Invasive Fruit Fly Pest, Bactrocera invadens: Concordance in Morphometry and DNA Barcoding}, journal = {PLoS ONE}, volume = {7}, year = {2012}, month = {May-09-2013}, pages = {e44862}, doi = {10.1371/journal.pone.0044862}, author = {Khamis, Fathiya M. and Masiga, Daniel K. and Mohamed, Samira A. and Salifu, Daisy and De Meyer, Marc and Ekesi, Sunday}, editor = {Filatov, Dmitry A.} } @article {4422, title = {Exploring Species Level Taxonomy and Species Delimitation Methods in the Facultatively Self-Fertilizing Land Snail Genus Rumina (Gastropoda: Pulmonata)}, journal = {PLoS ONE}, volume = {8}, year = {2013}, month = {May-04-2013}, pages = {e60736}, doi = {10.1371/journal.pone.0060736}, url = {http://www.plosone.org/article/info\%3Adoi\%2F10.1371\%2Fjournal.pone.0060736}, author = {Pr{\'e}vot, Vanya and Jordaens, Kurt and Sonet, Gontran and Backeljau, Thierry}, editor = {Steinke, Dirk} } @article {4414, title = {Genetic and Morphological Divergences in the Cosmopolitan Deep-Sea Amphipod Eurythenes gryllus Reveal a Diverse Abyss and a Bipolar Species}, journal = {PLoS ONE}, volume = {8}, year = {2013}, month = {Jan-09-2015}, pages = {e74218}, doi = {10.1371/journal.pone.0074218}, author = {Havermans, Charlotte and Sonet, Gontran and d{\textquoteright}Udekem{\textquoteright}d{\textquoteright}Acoz, C{\'e}dric and Nagy, Zolt{\'a}n T. and Martin, Patrick and Brix, Saskia and Riehl, Torben and Agrawal, Shobhit and Held, Christoph}, editor = {Fontaneto, Diego} } @article {4413, title = {Reliable DNA Barcoding Performance Proved for Species and Island Populations of Comoran Squamate Reptiles}, journal = {PLoS ONE}, volume = {8}, year = {2013}, month = {Dec-09-2013}, pages = {e73368}, doi = {10.1371/journal.pone.0073368}, author = {Hawlitschek, Oliver and Nagy, {\'a}n T. and Berger, Johannes and Glaw, Frank}, editor = {Joger, Ulrich} } @article {4392, title = {Island Evolution and Systematic Revision of Comoran Snakes: Why and When Subspecies Still Make Sense}, journal = {PLoS ONE}, volume = {7}, year = {2012}, month = {8/2012}, pages = {e42970}, doi = {10.1371/journal.pone.0042970.t001}, author = {Hawlitschek, Oliver and Nagy, Zolt{\'a}n T. and Glaw, Frank}, editor = {O{\textquoteright}Grady, Patrick} } @article {4384, title = {Identifying Insects with Incomplete DNA Barcode Libraries, African Fruit Flies (Diptera: Tephritidae) as a Test Case}, journal = {PLoS ONE}, volume = {7}, year = {2012}, month = {2/2012}, pages = {e31581}, doi = {10.1371/journal.pone.0031581.t001}, author = {Virgilio, Massimiliano and Jordaens, Kurt and Breman, Floris C and Backeljau, Thierry and De Meyer, Marc} } @article {4382, title = {Host Shifts from Lamiales to Brassicaceae in the Sawfly Genus Athalia}, journal = {PLoS ONE}, volume = {7}, year = {2012}, month = {4/2012}, pages = {e33649}, doi = {10.1371/journal.pone.0033649.t003}, author = {Opitz, Sebastian E. W. and Boev{\'e}, Jean-Luc and Nagy, Zolt{\'a}n Tam{\'a}s and Sonet, Gontran and Koch, Frank and M{\"u}ller, Caroline} } @article {4381, title = {First Large-Scale DNA Barcoding Assessment of Reptiles in the Biodiversity Hotspot of Madagascar, Based on Newly Designed COI Primers}, journal = {PLoS ONE}, volume = {7}, year = {2012}, month = {3/2012}, pages = {e34506}, doi = {10.1371/journal.pone.0034506.t002}, url = {http://www.plosone.org/article/info\%3Adoi\%2F10.1371\%2Fjournal.pone.0034506}, author = {Nagy, Zolt{\'a}n T. and Sonet, Gontran and Glaw, Frank and Vences, Miguel} } @article {4372, title = {Exploring the Use of Cytochrome Oxidase c Subunit 1 (COI) for DNA Barcoding of Free-Living Marine Nematodes}, journal = {PLoS ONE}, volume = {5}, year = {2010}, month = {10/2010}, pages = {e13716}, abstract = {Background The identification of free-living marine nematodes is difficult because of the paucity of easily scorable diagnostic morphological characters. Consequently, molecular identification tools could solve this problem. Unfortunately, hitherto most of these tools relied on 18S rDNA and 28S rDNA sequences, which often lack sufficient resolution at the species level. In contrast, only a few mitochondrial COI data are available for free-living marine nematodes. Therefore, we investigate the amplification and sequencing success of two partitions of the COI gene, the M1-M6 barcoding region and the I3-M11 partition. Methodology Both partitions were analysed in 41 nematode species from a wide phylogenetic range. The taxon specific primers for the I3-M11 partition outperformed the universal M1-M6 primers in terms of amplification success (87.8\% vs. 65.8\%, respectively) and produced a higher number of bidirectional COI sequences (65.8\% vs 39.0\%, respectively). A threshold value of 5\% K2P genetic divergence marked a clear DNA barcoding gap separating intra- and interspecific distances: 99.3\% of all interspecific comparisons were >0.05, while 99.5\% of all intraspecific comparisons were <0.05 K2P distance. Conclusion The I3-M11 partition reliably identifies a wide range of marine nematodes, and our data show the need for a strict scrutiny of the obtained sequences, since contamination, nuclear pseudogenes and endosymbionts may confuse nematode species identification by COI sequences.}, doi = {10.1371/journal.pone.0013716.t002}, url = {http://jemu.myspecies.info/sites/jemu.myspecies.info/files/journal.pone_.0013716-1.pdf}, author = {Derycke, Sofie and Vanaverbeke, Jan and Rigaux, Annelien and Backeljau, Thierry and Moens, Tom} } @article {4348, title = {DNA Barcode Sequence Identification Incorporating Taxonomic Hierarchy and within Taxon Variability}, journal = {PLoS ONE}, volume = {6}, year = {2011}, month = {8/2011}, pages = {e20552}, doi = {10.1371/journal.pone.0020552.t002}, author = {Little, Damon P.}, editor = {Kolokotronis, Sergios-Orestis} }