Abstract
Public DNA sequence databases such as GenBank are widely used for identification of organisms in ecological and taxonomic studies. It is important that these public databases contain as few mistakes as possible and that any errors detected in these databases are reported. Here, we reanalyzed the COI sequences of Mercan et al. (2024) and showed that they were mistakenly considered by these authors as belonging to different populations (haplotypes) within the species Potamothrix hammoniensis (Tubificinae). We found that they corresponded to four distinct Tubificinae lineages (species), Pothamothrix alatus paravanicus, Potamothrix bavaricus, Tubifex sp. and Potamothrix sp. Despite these identification errors, the data from Mercan et al. (2024) remain interesting as they provide new information on the diversity of the genus Potamothrix in Turkey. Prompt measures must be taken to correct these errors and prevent them from being detrimental to future studies.
References
- Carew, M.E., Kellar, C.R., Petitgrove, V.J. & Hoffmann, A.A. (2018) Can high-throughput sequencing detect macroinvertebrate diversity for routine monitoring of an urban river? Ecological Indicators, 85, 440–450. https://doi.org/10.1016/j.ecolind.2017.11.002 DOI: https://doi.org/10.1016/j.ecolind.2017.11.002
- de Queiroz, K. (2007) Species concepts and species delimitation. Systematic Biology, 56, 6, 879–886. https://doi.org/10.1080/10635150701701083 DOI: https://doi.org/10.1080/10635150701701083
- Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113. https://doi.org/10.1186/1471-2105-5-113 DOI: https://doi.org/10.1186/1471-2105-5-113
- Elbrecht, V., Vamos, E.E., Meissner, K., Aroviita, J. & Leese, F. (2017) Assessing strengths and weaknesses of DNA metabarcoding‐based macroinvertebrate identification for routine stream monitoring. Methods in Ecology and Evolution, 8, 1265–1275. https://doi.org/10.1111/2041-210X.12789 DOI: https://doi.org/10.1111/2041-210X.12789
- Gouy, M., Guindon, S. & Gascuel, O. (2010) SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Ecology and Evolution, 27, 221–224. https://doi.org/10.1093/molbev/msp259 DOI: https://doi.org/10.1093/molbev/msp259
- Harman, W.J. (1980) Specific and generic criteria in freshwater Oligochaeta, with special emphasis on the Naididae. In: Brinkhurst, R.O. & Jamieson, B.G.M. (Eds.), Aquatic Oligochaeta Biology. Plenum Press, New York, New York, pp. 1–8. DOI: https://doi.org/10.1007/978-1-4613-3048-6_1
- Hebert, P.D.N., Cywinska, A., Ball, S.L. & deWaard, J.R. (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B, 270, 313–321. https://doi.org/10.1098/rspb.2002.2218 DOI: https://doi.org/10.1098/rspb.2002.2218
- Hoang, D.T., Chernomor, O., von Haeseler, A., Minh, B.Q. & Vinh, L.S. (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Molecular Ecology and Evolution, 35, 518–522. https://doi.org/10.1093/molbev/msx281 DOI: https://doi.org/10.1093/molbev/msx281
- Ismailaj, M., Zangaro, F., Specchia, V., Sangiorgio, F., Marcucci, F., Kiçaj, H., Basset, A. & Pinna, M. (2024) Biodiversity patterns and DNA barcode gap analysis of COI in coastal lagoons of Albania. Biology, 13, 951. https://doi.org/10.3390/biology13110951 DOI: https://doi.org/10.3390/biology13110951
- Kalyaanamoorthy, S., Minh, B.Q., Wong, T. K. F., von Haeseler, A. & Jermiin, L.S. (2017) ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods, 14, 587–589. https://doi.org/10.1038/nmeth.4285 DOI: https://doi.org/10.1038/nmeth.4285
- Lawley, J.W., Gamero-Mora, E., Maronna, M.M., Chiaverano, L.M., Stampar, S.N., Hopcroft, R.R., Collins, A.G. & Morandini, A.C. (2021) The importance of molecular characters when morphological variability hinders diagnosability: systematics of the moon jellyfish genus Aurelia (Cnidaria: Scyphozoa). PeerJ, 9, e11954. https://doi.org/10.7717/peerj.11954 DOI: https://doi.org/10.7717/peerj.11954
- Liu, Y., Fend, S.V., Martinsson, S., Luo, X., Ohtaka, A. & Erséus, C. (2017) Multi-locus phylogenetic analysis of the genus Limnodrilus (Annelida: Clitellata: Naididae). Molecular Phylogenetics and Evolution, 112, 244–257. https://doi.org/10.1016/j.ympev.2017.04.019 DOI: https://doi.org/10.1016/j.ympev.2017.04.019
- Martin, P. (1991) Potamothrix Vejdovsky et Mrazek, 1902 (Oligochaeta, Tubifïcidae): un genre d’Oligochète dulçaquicole nouveau pour la faune belge. Belgian Journal of Zoology, 121, 315–320.
- Martin, P., Reynolds, J.F. & van Haaren, T. (2024) World List of Marine Oligochaeta. Potamothrix Vejdovský & Mrázek, 1903. Accessed through: World Register of Marine Species. Available from: https://www.marinespecies.org/aphia.php?p=taxdetails&id=137390 (accessed 22 August 2024)
- Martinsson, S. & Erséus, C. (2021) Cryptic Clitellata: Molecular species delimitation of clitellate worms (Annelida): An overview. Diversity, 13, 36. https://doi.org/10.3390/d13020036 DOI: https://doi.org/10.3390/d13020036
- Mercan, D., Arslan, N. & Korkmaz, E.M. (2024) Morphological‑genetic analysis of Potamothrix hammoniensis (Michaelsen, 1901) (Clitellata: Oligochaeta) with phylogeographic inferences: a case study in Türkiye. Biologia, 79, 803–814. https://doi.org/10.1007/s11756-023-01565-6 DOI: https://doi.org/10.1007/s11756-023-01565-6
- Michaelsen, W. (1901) Neue Tubificiden der Niederelbgebiets. Verhandlungen des Naturwissenschaftlichen Vereins zu Hamburg, 3, 66–70.
- NCBI Resource Coordinators (2016) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 44, D7–D19. https://doi.org/10.1093/nar/gkv1290 DOI: https://doi.org/10.1093/nar/gkv1290
- Nguyen, L.T., Schmidt, H.A., von Haeseler, A. & Minh, B.Q. (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32, 268–274. https://doi.org/10.1093/molbev/msu300 DOI: https://doi.org/10.1093/molbev/msu300
- Puillandre N., Brouillet S. & Achaz, G. (2021) ASAP: assemble species by automatic partitioning. Molecular Ecology Resources, 21, 609–620. https://doi.org/10.1111/1755-0998.13281 DOI: https://doi.org/10.1111/1755-0998.13281
- Schmelz, R.M., Beylich, A., Boros, G., Dózsa-Farkas, K., Graefe, U., Hong, Y., Römbke, J., Schlaghamerský, J. & Martinsson, S. (2017) How to deal with cryptic species in Enchytraeidae, with recommendations on taxonomical descriptions. Opuscula Zoologica Budapest, 48, Suppl. 2, 45–51. https://doi.org/10.18348/opzool.2017.S2.45 DOI: https://doi.org/10.18348/opzool.2017.S2.45
- 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. https://doi.org/10.1093/molbev/msr121 DOI: https://doi.org/10.1093/molbev/msr121
- Timm T. (2009). A guide to the freshwater Oligochaeta and Polychaeta of Northern and Central Europe. Lauterbornia, 66, 1–235.
- Timm, T. & Martin, P. (2019) Phylum Annelida. Class Clitellata: Subclass Oligochaeta. In: Rogers, D.C. & Thorp, J.H. (Eds.), Thorp and Covich’s Freshwater Invertebrates (Fourth Edition). Keys to Palaearctic Fauna. Academic Press, Boston, Massachusetts, pp. 364–482.
- Timm, T. & Abarenkov, K. (2024) Word distribution of the aquatic Oligochaeta. PlutoF. Occurrence dataset. Available from: https://app.plutof.ut.ee/ (accessed 22 August 2024)
- Timm, T. & Veldhuijzen van Zanten, H.H. (2002) Freshwater Oligochaeta of North-West Europe. Expert Center for Taxonomic Identification, University of Amsterdam, Amsterdam, World Biodiversity Database. [CD-ROM]
- Timm, T., Arslan, N., Rüzgar, M., Martinsson, S. & Erséus, C. (2013) Oligochaeta (Annelida) of the profundal of Lake Hazar (Turkey), with description of Potamothrix alatus n. ssp. Zootaxa, 3716 (2), 144–156. https://doi.org/10.11646/zootaxa.3716.2.2 DOI: https://doi.org/10.11646/zootaxa.3716.2.2
- Trifinopoulos, J., Nguyen, L.T., von Haeseler, A. & Minh, B.Q. (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research, 44, W232–235. https://doi.org/10.1093/nar/gkw256 DOI: https://doi.org/10.1093/nar/gkw256
- Vivien, R., Wyler, S., Lafont, M. & Pawlowski, J. (2015) Molecular barcoding of aquatic oligochaetes: implications for biomonitoring. PLoS ONE, 10 (4), e0125485. https://doi.org/10.1371/journal.pone.0125485 DOI: https://doi.org/10.1371/journal.pone.0125485
- Vivien, R., Holzmann, M., Werner, I., Pawlowski, J., Lafont, M. & Ferrari, B.J.D. (2017) Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database. PeerJ, 5, e4122. https://doi.org/10.7717/peerj.4122 DOI: https://doi.org/10.7717/peerj.4122
- Vivien, R., Apothéloz-Perret-Gentil, L., Pawlowski, P., Werner, I. & Ferrari, B.J.D. (2019) Testing different (e)DNA metabarcoding approaches to assess aquatic oligochaete diversity and the biological quality of sediments. Ecological Indicators, 106, 105453. https://doi.org/10.1016/j.ecolind.2019.105453 DOI: https://doi.org/10.1016/j.ecolind.2019.105453
- Vivien, R., Apothéloz-Perret-Gentil, L., Pawlowski, P., Werner, I. & Ferrari, B.J.D. (2020) High-throughput DNA barcoding of oligochaetes for abundance-based indices to assess the biological quality of sediments in streams and lakes. Scientific Reports, 10, 2041. https://doi.org/10.1038/s41598-020-58703-2 DOI: https://doi.org/10.1038/s41598-020-58703-2
- Vivien, R., Cermakova, K., Pawlowski, J. & Ferrari, B.J.D. (2023) OligoGen: Développement de méthodes oligochètes génétiques pour évaluer la qualité biologique des sédiments de cours d’eau. Centre suisse d’écotoxicologie appliquée Eawag-EPFL, Lausanne, 84 pp.